I have done them both ways - stuff them and freeze them and bake later or stuff them, bake them, them and defrost/eat later. Peppers stand up better to the freezing either way. I prefer to bake the stuffed tomatoes first before freezing. You get the flavour you want, although the texture of the tomato changes a bit more with the freezing/thawing.
Not sure if that's what you meant....but hope that helps.
Zana
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