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I've never used Typinator, and perhaps I wouldn't need to ask this question if I had: are you saying no matter what you type, pressing Tab causes Typinator to do an abbreviation, or is it simply that you happen to have Typinator abbreviations which happen to match the key sequences that are most convenient for some of your projects? If the latter, I'll point out that OmniFocus will match in many different ways, not just against the first characters of a word, so you can probably come up with different "abbreviations" for those projects which might even be more efficient than what you are typing now. Using some of the less frequently used letters appearing in the names instead of ETAOINRSH is often a good approach, and you may only need one or two to disambiguate from your Typinator abbreviations or other similarly named projects/contexts.

Because (as you noticed) OmniFocus usually doesn't appear to be the active application when the Quick Entry window is in use, I'm not optimistic there is a reliable code solution to be had from either vendor. If it turns out otherwise, I'd be interested to hear about it!