It would depend on which Arduino and what bootloader it's running. Generally MCUs have their pins in INPUT mode when they reset. Sometimes the bootloader will leave some pins configured for a particular mode by the some the sketch runs. E.g. the Leonardo seems to leave pin 13 set to OUTPUT mode.
You usually want devices connected to your Arduino to have stable signals when the Arduino MCU is in reset, or in the bootloader, so it makes sense to pull the signal pins, that will later be output from the Arduino sketch, to known levels. So maybe pulling your servo driver enable signal to inactive (HIGH) is appropriate.
Looking at the A4988, it has an EN (enable) pin, which seems to be active low. So putting a high(ish) value resistor, say 5k or 10k, on it to VDD/HIGH (to inactive) is probably the thing to do. When the Arduino is not driving the enable line to its low (active) state, that is when it's in the bootloader or being held in reset, the A4988 should stop its activity.