As always, I suggest giving my mbed-cmake tool a shot for any serious, long-term embedded project. First and foremost, it concentrates all dependencies in a single repo, removing some of the worries associated with how Mbed downloads/updates things from the Internet and guaranteeing that it will work exactly the same years in the future. Also, it lets you use almost any IDE you want (including VS Code and CLion, which are both very capable), or just build and upload code from the command line.
Also, re boards, my team has been using a custom PCB in our avionics unit for years, but we still have it configured in Mbed OS as the “dev board” for that chip. This works just fine as long as some of the basic PCB components (such as the clock IC) are the same type as on the dev board, but yeah if you wanted to changed those then you need a custom board.