I think the general opinion is that most APs are on the fairly difficult/unforgiving side, if run as written. However I feel most tables end up with some combination of more characters and/or free archetype tweaks on the character side of the equation that fine tunes the difficulty to fit the table's preference.
No one really knows how difficult this one will be- its just been pre-released after all. The 1e version felt "normal" for 1e, which in general felt about the same at low levels compared to 2e, but trivially easy for many high level parties. However I expect after encounters were updated for 2e, we'd be back at a slight higher baseline that should hold across all tiers of play.
In Kingmaker 1e "nova" classes were extremely strong; there were lots of 1/day encounters just as a nature of a hexploration based game. Of course there's still dungeons/complexes to deal with and you won't be always able to nova, but it was the most friendly AP to that style of game play.
The new intro on the other hand is very 'long haul'/resource constrained for most of your first level of play.
I wouldn't go in trying to increase the difficulty, you probably won't need to. But if you need to, the GM can add an extra opponent (generall an extra copy of a weaker thing already in the fight) or cautiously slap the Elite template on thing(s).
If using the companions, you should have plenty of people to cover settlement roles if undersized.
I can only address point #1, as I'm still not all that familiar with PF2:
The players have an advantage in this AP because a lot of the encounters and other challenges that the players face happen in an exploration scenario, and this AP usually only throws a maximum of one encounter at the party per day (not counting for random encounters). So this "five minute workday" the PCs have lets them blow their big spells and daily powers right away, often making the encounters trivial.
Individual encounters in a dungeon setting may be more lethal, because the PCs may deal with traps and multiple minion encounters before a boss encounter, all in a short period of time, but most of the encounters are otherwise open world.
As for lethality of the encounters, most of the encounters are very manageable... until they're not. It's hard to gauge this because of the randomness of die rolls, player decisions, and the fact that not every encounter in any AP has the same scale of danger. But in most APs, the encounters are grouped closer together than they are in Kingmaker.
(And all of the above assumes that the anniversary edition doesn't change this dynamic in some way I'm not seeing.)
Actually, for your second question, I can say that when I ran this AP for 1E, I had five players, so I used a fan-made conversion designed to increase the encounters for 6 players... and my players still had little trouble.
1. In my experience level 1 can be rough for players who aren't careful, once players start leveling it becomes much harder to wipe the party. Perhaps due to lenient GM'ing I've only ever seen one death. Failing quests is a harder metric since that depends on a mixture of player behavior and GM ruling. I'd say no more than other games and for AP's less because the adventure assumes you succeed.
2. Increasing the difficulty of monster encounters is easy - add more or make monsters elite. If you want to increase out of combat rolls increasing the DC by a single level is also very impactful.
There are nine roles for a kingdom and that is too many players for the average table so adding one more NPC to those roles won't be that impactful unless you make the NPC the ruler which I would regard as a wasted opportunity.
3. Action economy is the real power limit for the game. Dual classing does increase player options without question but there will be less impact than you might think because there are only so many actions and reactions you get as a PC per round.
With fewer players dual classing lets them cover the bases of a group without one player feeling they "have" to play a caster or a healer. The free archetype rule I wholeheartedly endorse for all size tables to help players realize their character concept and increase options during play.
I would avoid granting extra levels or withholding levels as the math might get wonky. It's ok to let your players get in over their heads but I never like holding my players back.
Increasing any roll target by 1 or 2 can have a huge impact on the game. Also letting your monsters play like PCs by utilizing skills and terrain elevates your game. You don't want to beat your players but your NPC's absolutely do want to beat the PC's and if you can strike that balance I think players will find your game challenging and engaging.
Good luck! As someone who left 4e for PF1e because I was not happy about the changes made by WotC I really enjoy running and playing in PF2e, I hope you do too.
If you like the idea of running with three players (or that's just youe group size!) take a look at the free archetype GMG optional rule, characters get archetype feats (which can be dedications and subsidiary feats) every even level. As I said I really do love that rule.