I’m going to be honest, the title does not make sense to me. I think you’re asking if it’s worth it to sacrifice “downward compatibility” (backwards compatibility?) if you get something out of it in exchange.
Well, fixOldSaves exists for this reason. If you need to rewrite a section you could choose to reset saves to the beginning of that section, or at least update their values to the ones they’d actually have at the section of the game they’re at.
If that’s not viable, then sure you could reset all saves (either via fixOldSaves or just changing the modid). I’d try not to do it when you don’t need to, though.