Is there any difference in the quality of a time remap coming out of the programs? Or is it another case of the program just being a tool to get the final result? Thanks ! :)

If it's of any help, i believe the Time Remapping plugin (for Premiere) was taken from After Effects..Maybe checking out some After Effects forums/Sub forums would get you more accurate answers.

Time remapping in FCP for me is indecipherable. It's hard to figure out how it works.

The same task in After Effects is very easy and straightforward.