Use the FMUv4 architecture to obtain double the flash. The first available board from this generation is the Pixracer.
The amount of code that can be loaded onto a board is limited by the amount of flash memory it has. When adding additional modules or code its possible that the addition exceeds the flash memory. This will result in a "flash overflow". The upstream version will always build, but depending on what a developer adds it might overflow locally.
region `flash' overflowed by 12456 bytes
To remedy it, either use more recent hardware or remove modules from the build which are not essential to your use case. The configuration is stored in /PX4-Autopilot/boards/px4 (e.g. PX4-Autopilot/boards/px4/fmu-v5/default.cmake). To remove a module, just comment it out:
On Ubuntu, uninstall the modem manager:
sudo apt-get remove modemmanager