Hah, you haven't experienced the HoI4's heyday when Drikus/Bratyn was still here. He designed the Dutch contents for MtG from what he learned on his graduate and master programmes on history.
The problem is fundamentals, not so much details.
With regards to focus trees, I do believe that Japan could become communist or the US could have a Second Civil War in the 1930-1940s.
Focus trees are not really the problem.
The bigger problem are underlying game mechanics that apply to all countries. For example:
1. Artillery is inferior to tanks in every single way on a per width basis.
2. Infantry can move at a speed of 96 km/day, when in reality normal speed would be 35 km/day under ideal conditions.
3. Land cruisers are a viable unit.
4. A country can multiply its economy over a course of a couple of years (makes me think of Age of Empires/Cossacks series of games).
To compensate patchwork modifiers like "Ichi-Go" in China or "Unplanned Offensive" in Spain get invented, because otherwise the war will end too soon.
Bad design philosophy -> bad design choices -> stitches and patches to make the thing run in some way
Or even history buffs from other countries who has little representation in WW2 games making contents for their country in HoI4 like me (see East Indies Reworked mod, i made it) and that Portuguese professor who helped design Portuguese content for La Resistance.
I'll check your mod out, just to get a feel a what I don't know about that area. I can say in advance though, the data I collected shows Dutch East Indies were roughly economically equal to the metropolitan Netherlands. Would be interesting to compare that to what I see in your mod.
With regards to Portugal, I did hear some criticism about their focus tree.
Certainly while there is small overlap between modders and history buffs, i think we did great to provide well-researched contents, both historical and plausible alt-history ones nonetheless.
I kind of feel the tools available to represent small countries are very limited. HOI4 economies are condensed to military factories, civilian factories and industrial resources. If you compare this to Victoria 3, all agricultural and exotic goods are left out, distorting the picture.
For example, the Balkans were extremely important for Germany because of their tobacco industry. Bulgarian tobacco saved German smokers in WW1.
Vietnam, Mexico were major producers of opioids that were necessary for painkiller production at the time.
Minor countries have no real way of showing their true importance within the context of HOI4. You just don't have the tools.
If "plausible alt-history" is "what kind of crazy name can come to power" it's kind of hard to call that "Alt-history" as it doesn't really change much.
Ok, you put "The Non-Aligned guy" instead of the "Fascist guy" in charge: you get some wargoals (which shouldn't be tied to ideology in the first place) and maybe some overpowered modifiers that have no ground in reality. If you don't do that, you get pure cosmetics like portrait & flag changes.
You don't feel actual changes in internal politics depending on decisions you make, it's just "change a flag and get a claim on territory X". Not really meaningful.