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No religion and no culture actually still converts to your own culture and religion even in a trade company region
Unfortunately some province history files weren't updated though but that should be taken care of with the next patch (now an empty province *should* have noreligion and noculture). I also removed natives from some islands that shouldn't have them for this reason while going over that.
As for gameplay/realism. I believe what the OP actually asked for wasn't a gameplay explanation "did my colonists get jungle fever". I can only reply about stuff that's my department, and flavorwise wiping out entire populations is not really realistic in most trade company regions. Gameplay wise as to why this applies to trade company regions and not others isn't something I'd be the right person to answer. I agree it's not very convinient for countries that can't actually have trade companies as I'm mostly a ROTW player myself.