Omar, I've restored both ways, once through a hard restore, and once through a reset from the server. I had to restore because I downloaded the 'sneaky-peek' iPhone 2.0 for my 1st gen iPhone, and had to manually restore to get the 'legit' OS on launch day. When you restore, the process first wipes your phone and installs the new OS. You then sync with iTunes, and everything (music, apps, etc.) is restored to the previous state, minus some local preference settings that are reset to default. All of my apps, including OF, were restored with no problems.
I'm probably not the best case for your question as 1) I have not experienced any crashes with iOF (other than it is a little slow with my 7MB db), and 2) I sync to MobileMe and I can't remember whether I had to re-sync or not. I'm sure someone at OG has tested the restore process with a stand-alone setup like yours.
An interesting question would be if your phone was damaged and you had to get a replacement, would it replicate the contents on the new phone? (I poured water on one, not recommended.)
One thing that is frustrating is that Apple is adamant on making all iPhone apps stand-alone, i.e., they should not depend on, or merely be an extension of, a desktop app. If this is the case, why don't developers have any access to the wired sync process (Ken says the wire is off limits), and why don't we have a 'restore' or 'backup' button in iTunes for each app? I keep a lot of client data in my OF db, and am concerned about data integrity like you. Is my data fully backed up or not? After all, it is MY data! Where does it go?
But as you said, transparency is a four-letter word at Apple... So for now I just hit sync 300 times/day ;)