no idea, but I imagine having the DLC data installed on your HDD would make it a lot more stable than the disc-based GOTY edition.
Hey, you're from my hometown!
Unfortunately I don't know how this could make sense. GOTY comes with a separate disc that contains all the additional content that you then install from it. You can't play off that disc. Onc eyou install it, you have to put the FO3 game disc back in. It gets installed right onto your HDD.
The only thing I noticed was that the game maybe ran a little bit slower, and there were some bugs like floating objects, but I found out I needed to clear my game cache (I play on the 360) and it's run fine since.