If, for example, AI Germany (miraculously) becomes monarchist but loses the civil war, Hitler's Germany will lose the unique German focus tree and keep a generic focus tree. The lack of warmongering and proper World Tension means a broken game no matter who you play as.
It has been stated that this has been resolved (though I can't remember where...
For some reason, setting the AI to be truly Random (rather than following Default weights or 100% going down a certain path) will deactivate achievements (as you can verify in the latest DD).
It's a considerable punch-in-the-face for fans of alternate history (in a Paradox game, who would have guessed) and in fact makes little sense, as a player wishing to restart multiple times just to randomly get the ideal setup for an achievement run may just as well use the effort to cheat Steam's achievement system in a myriad ways, all being far faster.
Said 'some reason' is that the various default weights and scripted AI strategy plans take into account what other nations have done. E.g. if Imperial Germany expels the communists, France is guaranteed to go Communist to serve as a counterweight, and if Germany goes democratic, France will go fascist and ally Italy for precisely the same reason (ensuring there is always a war happening).
The "Random" setting for the custom game rules overrides this completely. It randomly selects from the strategy plans we have created for the nation in question, and no matter what other nations do or what we scripted the strategy plans to take into account the country will continue to follow the strategy plan that was selected, in a similar manner as manually selecting specifically that path in the custom game rules would do. As you might imagine, this causes all sorts of potential issues that the 'default' weightings and triggers we implemented were designed to avoid. You could hypothetically end up in a situation where no WW2 occurs at all, or where two nations end up in the same faction despite this going expressly against the storylines for their respective paths. These unintended paradoxes would greatly mess with achievements, which is why they were disabled for anything other than historical mode or the original 'default' random mode (i.e. "Historical AI Focuses" option turned off). I'm sorry that you experience this as a 'punch in the face'.
We still don't know how random Random mode will be in first place, despite two dev diaries on Custom Rules. Will e.g. the Netherlands have a perfect 25% chance of becoming communist, fascist, democratic or Non-Aligned? Or will some weights still be in place?
I hope that the above explanation for how these rules work sheds some light on this question, too. No weights are in place when selecting random - it follows the scripted focus path. As for the chance for specific paths to be selected, it roughly follows an even distribution between the various possible paths, though some adjustments have been made for 'coolness' and 'entertainment value'. I.e. Machukuo is slightly more likely to go independent than remain loyal to Japan, but the difference is not very great between these. The chances are also easily adjustable by modding, if you prefer different values.