I've got hundreds of QuickTime MOVs with embedded timecode, and they work just fine in Premiere Pro. I don't recall having any MPEG files with timecode, so I'm not sure what you're referencing there. AVCHD timecode requires the folder structure, since the timecode and other metadata (e.g. spanning) are not written into the video files, but is instead inside other files in the structure.
Bottom line is that I've never had problems with Premiere Pro reading timecode information where timecode information is present.
Interesting, I haven't been able to get Premiere to read timecode in MOV files. What version of Premiere are you running and on what OS. Would it be possible to upload a sample MOV you have with timecode in it so I can see its structure?
Here are a couple: http://www.mediafire.com/?1c145kclvm1tf1v
They're Panasonic P2 DVCPRO HD MXF clips that are rewrapped via FCP's Log and Transfer (they were for another test). They show timecode (same as was shot in-camera) in CS5 and CS5.5 on Windows.
I can probably dredge up some other clips if needed.