As I understand, and have no legal knowledge other than if pay your parking tickets, you do not get into trouble.
but some if not all, of these free use licenses, state that any work that is a derriviative of that , or use that, are with the agreement that the work is also open and free.
but to put all this aside, It is doubtful that you will invent a patenatable software routine that cannot be achieved by a clean sheet approach.
to be on the safe side, what your prof was saying is that if you use the arduino bootlodader in your for-sale product, that you may be a derrivitive work.
if you learn actual C or C++ or ASM, or even FORTH, you can program your chip in one of those without any roots in the Arduino world.
there have been many people who develop in the Arduino world, then just re-write the programs in some other language for different reasons. one is speed of execution. another is to get access to tools not available when using the bootloader.
so, first off, don't reveal your patentable secrets,
Then when you think you have that better mouse trap, write it in a way that does not use the Arduino boot loader and that way you eliminate the possibility of the issues you fear.