Strongly feel the logical progression is: (1) Wiring third party devices and modules to an existing MCU board and programming it (2) Making a PCB to plug modules and the MCU board in to (3) Making a PCB with integrated peripherals and only plugging the MCU board (4) Making making a whole board with everything.

The MCU is typically far more fiddly than the devices (eg. crystals, storage, buses with conditioning, power stages, etc.), so continuing to plug the MCU in to a PCB while integrating peripherals is a good. You really need to be able to read a datasheet to do a nontrivial board and that brings in quite a few elements of electronics which are nontrivial for kids to grok without hand-holding and a lot of explanation.

Pick an MCU with easy USB-C programming. RP2040 is a good modern option.