In the Arduino IDE do this:
- File > Preferences > Show verbose output during: > upload (check) > OK
- Tools > Burn Bootloader
After it finishes examine the output in the black console window at the bottom of the Arduino IDE window. If you look carefully you'll see that the Arduino IDE actually runs two separate AVRDUDE commands when you **Burn Bootloader**. The first sets the fuses according to the settings in boards.txt for the selected board, the second actually burns the bootloader. So your comparison is not really fair unless you run both commands in your test of using AVRDUDE directly.
##Edit by OP:
Full output in the Arduino IDE:
D:\Programme\Arduino\hardware\tools\avr/bin/avrdude -CD:\Programme\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega32u4 -cstk500v1 -PCOM4 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m
avrdude: Version 6.3, compiled on Sep 12 2016 at 17:24:16
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch
System wide configuration file is "D:\Programme\Arduino\hardware\tools\avr/etc/avrdude.conf"
Using Port : COM4
Using Programmer : stk500v1
Overriding Baud Rate : 19200
AVR Part : ATmega32U4
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PA0
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
eeprom 65 20 4 0 no 1024 4 0 9000 9000 0x00 0x00
flash 65 6 128 0 yes 32768 128 256 4500 4500 0x00 0x00
lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00
Programmer Type : STK500
Description : Atmel STK500 Version 1.x firmware
Hardware Version: 2
Firmware Version: 1.18
Topcard : Unknown
Vtarget : 0.0 V
Varef : 0.0 V
Oscillator : Off
SCK period : 0.1 us
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.02s
avrdude: Device signature = 0x1e9587 (probably m32u4)
avrdude: erasing chip
avrdude: reading input file "0x3F"
avrdude: writing lock (1 bytes):
D:\Programme\Arduino\hardware\tools\avr/bin/avrdude -CD:\Programme\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega32u4 -cstk500v1 -PCOM4 -b19200 -Uflash:w:D:\Programme\Arduino\hardware\arduino\avr/bootloaders/caterina/Caterina-Micro.hex:i -Ulock:w:0x2F:m
Writing | ################################################## | 100% 0.01s
avrdude: 1 bytes of lock written
avrdude: verifying lock memory against 0x3F:
avrdude: load data lock data from input file 0x3F:
avrdude: input file 0x3F contains 1 bytes
avrdude: reading on-chip lock data:
Reading | ################################################## | 100% 0.01s
avrdude: verifying ...
avrdude: 1 bytes of lock verified
avrdude: reading input file "0xcb"
avrdude: writing efuse (1 bytes):
Writing | ################################################## | 100% 0.01s
avrdude: 1 bytes of efuse written
avrdude: verifying efuse memory against 0xcb:
avrdude: load data efuse data from input file 0xcb:
avrdude: input file 0xcb contains 1 bytes
avrdude: reading on-chip efuse data:
Reading | ################################################## | 100% 0.01s
avrdude: verifying ...
avrdude: 1 bytes of efuse verified
avrdude: reading input file "0xd8"
avrdude: writing hfuse (1 bytes):
Writing | ################################################## | 100% 0.01s
avrdude: 1 bytes of hfuse written
avrdude: verifying hfuse memory against 0xd8:
avrdude: load data hfuse data from input file 0xd8:
avrdude: input file 0xd8 contains 1 bytes
avrdude: reading on-chip hfuse data:
Reading | ################################################## | 100% 0.01s
avrdude: verifying ...
avrdude: 1 bytes of hfuse verified
avrdude: reading input file "0xff"
avrdude: writing lfuse (1 bytes):
Writing | ################################################## | 100% 0.01s
avrdude: 1 bytes of lfuse written
avrdude: verifying lfuse memory against 0xff:
avrdude: load data lfuse data from input file 0xff:
avrdude: input file 0xff contains 1 bytes
avrdude: reading on-chip lfuse data:
Reading | ################################################## | 100% 0.01s
avrdude: verifying ...
avrdude: 1 bytes of lfuse verified
avrdude done. Thank you.
avrdude: Version 6.3, compiled on Sep 12 2016 at 17:24:16
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch
System wide configuration file is "D:\Programme\Arduino\hardware\tools\avr/etc/avrdude.conf"
Using Port : COM4
Using Programmer : stk500v1
Overriding Baud Rate : 19200
AVR Part : ATmega32U4
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PA0
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
eeprom 65 20 4 0 no 1024 4 0 9000 9000 0x00 0x00
flash 65 6 128 0 yes 32768 128 256 4500 4500 0x00 0x00
lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00
Programmer Type : STK500
Description : Atmel STK500 Version 1.x firmware
Hardware Version: 2
Firmware Version: 1.18
Topcard : Unknown
Vtarget : 0.0 V
Varef : 0.0 V
Oscillator : Off
SCK period : 0.1 us
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.02s
avrdude: Device signature = 0x1e9587 (probably m32u4)
avrdude: NOTE: "flash" memory has been specified, an erase cycle will be performed
To disable this feature, specify the -D option.
avrdude: erasing chip
avrdude: reading input file "D:\Programme\Arduino\hardware\arduino\avr/bootloaders/caterina/Caterina-Micro.hex"
avrdude: writing flash (32730 bytes):
Writing | ################################################## | 100% 35.65s
avrdude: 32730 bytes of flash written
avrdude: verifying flash memory against D:\Programme\Arduino\hardware\arduino\avr/bootloaders/caterina/Caterina-Micro.hex:
avrdude: load data flash data from input file D:\Programme\Arduino\hardware\arduino\avr/bootloaders/caterina/Caterina-Micro.hex:
avrdude: input file D:\Programme\Arduino\hardware\arduino\avr/bootloaders/caterina/Caterina-Micro.hex contains 32730 bytes
avrdude: reading on-chip flash data:
Reading | ################################################## | 100% 19.92s
avrdude: verifying ...
avrdude: 32730 bytes of flash verified
avrdude: reading input file "0x2F"
avrdude: writing lock (1 bytes):
Writing | ################################################## | 100% 0.02s
avrdude: 1 bytes of lock written
avrdude: verifying lock memory against 0x2F:
avrdude: load data lock data from input file 0x2F:
avrdude: input file 0x2F contains 1 bytes
avrdude: reading on-chip lock data:
Reading | ################################################## | 100% 0.01s
avrdude: verifying ...
avrdude: 1 bytes of lock verified
avrdude done. Thank you.