I recently came across your review on youtube for this system, are you sure about hating on perks/flaws and skill choices if it's just how they often get thrown into a rules book as a loose jumble? I'm wondering if borrowing from Traveller and 5th D&D can sort those issues out.
Traveller has usually had homeworlds to choose during character creation which affects your skills loadout, so for the system you've reviewed here maybe you can package some skills by your dangerous terrain of origin and others by your specific settlement or shelter within that region. Something about the way Traveller handles skill levels could also bypass the fiddly point buy. The same thing could be done using psyche-profiles as a kind of background option with archetypes, these profiles would get a set of perks and flaws that are pre-balanced and flavorfully consistent.
It might be tougher to justify some skills this way, pick pocketing for example needs a high traffic area which is usually very populated, barring some wealthy enclaves or a market defended with some effort. High-tech skills like computers would be mostly alright, since a factory can be powered with rivers at least, or slaves mining coal where that isn't possible, or whatever else is going on.
And if a player wanted a slightly modified version of any those packages, they can always ask their GM about what would be traded out and if that would break anything before settling on an approval or counter-proposal.