Hi vinkandoi!
Mods leaving traces in the save games was is often pointed out as a problem by players and we took note on that.
As for 3rd party mods, there are excellent mod managers to help you with that, for example:
http://www.train-fever.net/filebase/index.php/Entry/486-Train-Fever-Game-Manager/
http://www.train-fever.net/filebase/index.php/Entry/5-TFMM/
Best Regards
Tom