I thought it was a nice that when you run Oblivion from Steam, it will go ahead and use OBSE if is installed. Centralizing/intergrating things is always a good thing. Hope it will be possible with Skyrim too.

I don't think that was a Bethesda thing, but rather a Valve thing.

That's a trick done by the script extender INIs, not by Steam, IIRC. Also, IIRC, it started causing issues in FONV, with NVSE not loading properly if you load via the launcher instead of straight with the SKSE loader.