This makes me wonder, what if, even in a reputable casino, RTP version can be tweak like this, so for example, a casino can claim they are using the 96% RTP slot version of a slot, but it could actually turn out to be the lower version. Can this be a posibility?
Yes, that's possible whether by mistake or deliberately. Best you can do is to compare the rtp in the official website (if it is stated) and the casino in question, I suppose.
As much as possible, always go with reputed casinos and providers as we still have to trust them up to a certain extent.