True. One more thing to mention is that this mod lets you rotate through half of the available starting locations. Honestly, I don't know how much it shuffles the other civs ==> how much it causes the bizzarities you mention.
So maybe if you (for example) "steal" a starting location of Aztecs in jungle, the game will (probably) try to place them in another available jungle start, which might kick out another jungle-biased civ to a completely random start like tundra. No idea.
I usually play with crowded (huge) maps, so I think some oddities would be still be happening, but I do not see them too often.
I have no idea if I only end up stealing the position of one of the civs, but I've seen a few games where 3 or 4 civs were 'displaced', of course map generation is pretty random, so these might just be coincidences, but I'm noticing it a lot more when I'm using the mod.
By the way, G, how about this?
Kinda off-topic, but could we please change the default-settings to disable tech-trading and enable research-agreements? I fear it is really confusing for first-time users, and also tech-trading is a Civ4D feature, it is there for fun but it is hardly a balance-improvement (probably actually the opposite)