There are two different reasons for a second MCU on a development board.
1) If the main MCU has a bootloader for serial upload, but doesn't include USB peripheral and the dev board should have for convenient development an USB port, then the board must include a USB-to-TTL-Serial adapter ('FTDI'). The adapter can be an FTDI USB chip, some other manufacturers USB chip (most common is CH340) or an MCU (with a USB peripheral) programed as USB-to-TTL-Serial with a firmware. Original Arduinos use ATmega 8u2 or 16u2 for this.
2) Some dev boards include a programmer for upload without bootloader. The programmer is a second MCU running a programmer firmware and is wired to programming pins of the main MCU. For example Arduino Zero, M0 Pro or Uno WiFi Rev 2, Nano Every have this concept.