My understanding (and it appears to be borne out when I try it) is that if you stretch a clip, and then go to the clip's properties panel and turn the rendered stretch mode off, it will give you the opportunity to save the stretched clip when you close the session, as it's effectively part of a file with a change that hasn't been saved. And when you reopen the session, there it is - already rendered. The other thing you can do with a stretched clip is to convert it to a unique copy (that's a right-click option on the clip itself) and that will give you a unique copy of the stretched clip - which you save as such.
The situation appears to be that if you've turned rendering off for a clip, it won't get rendered. So, if you've already rendered it, then it won't render again. That makes logical sense, but I'll be the first to admit that I've only tried this on a single clip as an experiment. But it does seem to work, and I didn't get any attempts to re-render the clip, either on reopening the session or, just as importantly, mixing it down/exporting it.
As for the situation with OMFs, I don't know. But there's a chance that SuiteSpot might - hopefully he'll see this and comment.
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