Hi @steve5528
You are right, that's because these examples are typically not configured using the MCUXpresso Config Tools , but instead use manually written SDK-provided functions for the EVK.
The board setup code for lpcxpresso55s28_usbx_device_hid_mouse was not tool-generated using MCUXpresso Config Tools. The board initialization is done using standard SDK calls.
For a custom board, generate your own .mex project with MCUXpresso Config Tools and bring in USBX source files.
BR
Harry