1) Because it makes sense according to game mechanics.
2) Because, as others have said, realism cuts both ways.
1) On what planet does it make sense to prioritize low tax distant overseas provinces that will never lend any trade value to the nation colonizing them? ROI on paying ducats for such a colony there is so terrible that any alternative location that either adds to a CN or allows them to collect trade is stronger. On top of all that, the strategic value is junk too (further conquest of the region is poor for the same reason that colonies there are poor, while there are myriad better ways to attack China if that's the goal that *do* give trade value). On top of all that, it gives Russia an easy CB that the Iberians can't really defend. Where's the upside? Where's the "it makes sense"? Usually people don't assert that making poor RoI investments with large opportunity costs makes sense.
2) Realism does cut both ways. Let me ask you though, what are you designing the game to be? Fun right? Remember that part about it being a game

? Rebels aren't fun. They're asinine tedium that also test the limit of plausible game balance (extremely evident in the case of minors getting large revolts or rebellions larger than their FL). I sincerely hope you've given the spawn #'s very careful consideration such that it isn't literally impossible to avoid losing territory at random to events. There's nothing a 2 province minor can do to 15 regiments on defensive terrain with a shock 3-4 general, and that kind of garbage happens right now. If you're going argue rebels from a gameplay sense, they still need work and stategem's OP is a good example of why even disregarding the historical population values. Rather than juicing rebels to the point where you can literally kill millions of men in 10 years and see millions more in the next, perhaps it would have made more sense to simply make the practical resources of expansion a stronger constraint or to lower the RoI of expansion against alternatives :/.
It would have made a lot more sense that as your nation grows its bureaucracy allows less FL/money/manpower growth, and this creates some decisions wrt gameplay incentives too. But what do we get instead? Rebels over a 5 year period that can match Napoleonic armies, in difficult-to-reach boondocks. "Both ways" indeed.
Unless Qing does it, then it's perfectly fine.
? Qing is orange. Not just a little orange either. Disgustingly bright, beautiful orange.
Basically, colonizing Siberia before tropical places makes sense because tropical is more punishing. Maybe we should change the fact that Siberia is a better place to colonize than much of Indonesia, but solving it by having the AI make poor decisions because they are 'historical' is not the way to go.
Tropical is more punishing, but it also gives what, 10x the value or more? The Indies have several times the tax per province, better value goods, and the Iberians actually *CAN* see trade from them.
Not to mention that literally any province in the new world gives more direct and trade value also. The new world is *not* filled by the early 1600's. Why are they putting colonies in Siberia? Does Siberia have 10 tax provinces in your internal build such that the value proposition of that is drastic enough to merit colonies in an overseas demerit region with 0 trade upside

?