is a PWM on Pin X with Value 100 different from PWM on PinX with Value 100 on 18,432 if compiled with 18,432 in Boards.txt?
The short answer is - Yes it is!
If you give it some thought - you can probably answer how and why that is yourself. 
The follow up would likely be - Is it relevant? - and that is also for you to determine as it depends on your project requirements.