I can't for sure say something about the other parts (other than that you may have other things like artifacts or advancements that lowered the actual percentage of additional gain: in general, if you have two increments of 15% each, your total income only goes up to 30% (15+15) not ~32% (1.15*1.15=1,3225 -> 32.25% increase); and your money income is already a combined number of territories and bonuses, so later techs will appear to give less benefit), but I'm pretty sure you misinterpreted what happened with:
And there is another bug : this upgrade doesn't run for the future bonus territories income.
Can't guarantee you this, but I'm very confident that the increment is already applied to each bonus as it is written on the map, so as soon as you complete a new bonus, you should get the extra 20%.
There is a bonus you don't have yet that grants you 1k. After you unlocked the tech, clicking on the bonus should tell you 1.2k (*) and completing it should you give you that 1.2k.
(*) the numbers on the map could be static, hence, not change after unlocking the tech, but that still should show correctly in your money balance.
And always take into account that most of the numbers in the idle game are rounded to some extend. So a low percentage increase might just not show up at all.
I just started another level and I will check what I can say about Geopolitics as soon as I have the items for the bonus income tech.