Welcome to the forums.
1. I understand from some comments in this forum's threads that non-fighters, non-spellcasters can still have something to do during fights. My question is: what? What options do you use to build these PCs to be effective and fun? Are these specific feat chains, tricks or something else that I'm missing? I'd love to get some examples as to what kind of identity - which is both powerful and intereting! - can classes like Sages/Courtiers/Keepers build for combat encounters.
Feint, Grapple, Taunt, Threaten and Tire are all skill based - which means that BAB is totally irrelevant (and as such they are equally useful to a Soldier and a Keeper). They are also available to anyone - no feats required. Further, there's less of a Defence ramp up for enemies, so 3/4 BAB progression is actually the standard for hitting folks, rather then full - this makes the Sage, Assassin, Burglar, Scout and so on perfectly fine in combat. For the non-attack bonus based options there are options to make it better (Menacing Threat / Glint of Madness for Threaten, as well as Beguiling / Aggro for Taunt). While a Courtier will never match a Soldier in combat (their class abilities are aren't designed for combat, compared to a class full of combat abilities) they can certainly contribute - and if built to maximise combat options (Menacing Threat + Glint of Madness + Enlightened Intimidate) they can do extremely well.
2. Armor in pretty much all D&D editions is pretty boring. Each class has their optimal armor type and unless you're wearing this armor, you're simply hurting yourself. Even classes that are supopsed to be "in between", like rogues or rangers, have the one specific kind of armor that was obviously written with them in mind, some games going so far as to specifically mention them in the classes abilities. Is it like this with this system as well? Are there other paths to take? Can a reasonable munchkin build a Soldier or a Lancer wearing anything other than the heaviest armor they can find? How about other classes?
Since armour is DR and higher DR often has higher Defence Penalty and Armour Check Penalty you do have to find a balance, and at my table I've seen both extremes as well as the far more common middle. The guy in Padded (no penalties), with a Guard weapon and a high defence class vs the guy in super heavy armour with around Defence 10, but huge DR. The most common things are Boiled Leather and Chain - both have a nice balance between DR and penalties. I've played both extremes too, and neither is categorically "better".
3. What good is alignment damage? It appears as a benefit in many places in the book, but I couldn't find the actual mechanical effects for it. What am I missing?
It's not really spelled out well, I'll admit. The Outsider type suffers (and inflicts) +2 damage from attacks with an opposing alignment. That's the default level - I'm pretty confident it exists for GMs who have specific needs for their worlds to use for additional effects.
4. Be honest now - how modular and full of options is this game, really? How much fun can you have building characters here, while still retaining that warm munchkiny satisfaction from knowing that your adventurer can get the job done? It's a bit of a reiteration of points 1 and 2, but in a more general sense. Did you ever build an off-the-beaten-path PC that still felt powerful? What options did you utilize?
I've been gaming for a long time now, so I all but exclusively try out different combinations (though not for any sort of "munchkiny satisfaction" - since I'm not entirely certain what that is). I've played the above Courtier + Threaten machine and it was a powerhouse until my GM (at the time) got annoyed and we exclusively fought things immune to Stress damage. I've played a Scout Sniper (a role most people would assume would fall to Soldier), a Martial Artist that never used his fists. All did well and were fun to play (but I GM more then 10x as often as I play, so I don't have many examples).
On the GM side, I've run: Classic Fantasy (think D&D), Industrial Fantasy (Steampunk), Warhammer 40k, Mass Effect, and I'm currently running Stargate. So yeah, there's a fair bit of modularity (though I will happily admit I made up a heap of rules for the last 3 settings - not exactly "out of the box").
Like Coyote0273, I've had 2 players at the same time as a Soldier who were totally different - one was a tanky style Greatsword guy with huge DR and strength and the other was a nimble fencer with high defence and dexterity, but was far squishier - both "Human Soldiers".