These two drivers are identical.
This is an 8-bit / 16MHz processor, think Arduino Nano.
This is an 8-bit 24MHz processor, think Arduino Mega.
The drivers are identical but your “newer” board brain is somewhat faster/bigger (not too much) than the “old” board brain.
This is entirely due to the code running on the board. The second “new” board should be able to perform better, apparently however, the code is worse. Go figure.
Seems very doubtful. The min/max speeds are entirely dependent on the code executed and I do not believe that switching from a potentiometer to PWM would change internally the RPM min/max scaling. However, since yo do not know the algorithm, it may be worth trying, but no guarantee at all. This whole thing as you can tell is very random.
Cheers,
Valentine