Swappolube works in a bit different way ... it change the value after it is loaded from the rcS file... instead MaeModder change the rcS ...
So no incompatibility ... but the swappolube value will "win" over the Maemodder one.
No problem with tracker cfg...
Some problems could occur with transition control ..
Maemodder simply copy one of the selected transitions file in the directory (there are the bests for me .. ) ...
Instead transition control read every value of the transition file... i don't know how it works but it seems that it works with positional parameters...

So if i change the position of a value... transition control crashes... and often the custom transition files have some parameters in different positions respect to the original..
So using a custom transition file , transition control could crash, but nothing more
It should return working restoring the original file.

So no big incompatibilities