I don't know anything about Sonar 7, but I'd suspect that this system will be pretty much the same as other packages of the type.
I think I understand what you're talking about. You record your music, and the system applies all sorts of 'adjustments' to what you've played to 'fit' the recording to a 'correct' structure. Whether you like it or not!
I have some old DOS systems that either did not do this, or did not do it so drastically, and the midi file created can still be a total mess, with notes all over the place, tiny notes (1/32 or even 1/64ths) cluttering the place up, notes (in effect) spread over bar boundaries, etc, etc. OK, I'm pretty CRAP with any keyboard/playing, but I'd suspect that even a good player will have problems.
Sounds like you want to do the initial recording in a 'raw' form, maybe you need to make sure that any sort of Quantise (quantize ?) is off, or maybe you need to change the resolution setting from the default untill you get a better result.
NB - the system is TRYING to HELP you, of course. By adjusting the notes to fit the bars/tempo. This will be very difficult to adjust after the recording is done. It's probably a matter of allowing some level of adjustment (to keep things approx within tempo etc) and then doing some small adjustments afterwards?
I'd be interested in trying one of your files. To hear how it sounds, and see what it looks like. It may well SOUND a LOT better that it LOOKS??
I suspect that if a composer wrote his score, and then played the piece and recorded it using midi, and then printed out the resultant score, it would look VERY LITTLE like his original written version? No matter how carefully he was trying to play it??