I have plenty experience, & plenty of problems with other games. It does some proprietary things which are stupid. It does alter directory structures, maybe not in this game, but ive seen it. Havent used it in awhile, partly because most games on it are screwed up.
And yes, people are explicity having problems with the steam version, read some posts if you dont belive me.
The core patch to the game is the same yes, but it requires extra proprietary crap which is almost always bad.