Couldn't you put related tools on top of their clothes? E.g., a blacksmith has a tool belt over their clothing. You could also give them a color-coded sash instead of coloring their whole outfit.
A coloured sash was
my thought earlier in this thread (or micro-tabbard/whatever, sufficient to be seen even over similarly-hued underlay, but not to be deemed 'clothing'), then I morphed this idea into maybe an
effect like an aura,
halo or some sort of floating hula-hoop band around them at a handy height. If animated enough to demonstrate its disconnection and lack of ingame reification.
Or, if a sash, one sash-orientation (\) could be civilian, the other one (/) could be military. Heck, you could even retain any [civ|mil] sash as a subordinate layer when they don the [mil|civ] one, according to any rule of significance you care to apply (master+ of a profession retains the indicator, say, when on militaey duties just to stand out from mere dabblers in anything non-military conscripted for their weapon proficiencies). It could also mix and match the current wielded weapon (or tool) with the
actual expertise(s?) they have.
But that's far too complicated, I'm sure. I'm not even even your primary market for all of this gorgeous-looking graphical bounty, I'm afraid, so take my admiration for the work, please, but you don't need to bend over backwards to try to apply my 'solutions' to what I know is going to be a hard thing to implement within such a narrow span and height of pixels.
I see someone also mentioned shadows of tree-tops (to distinguish them from stumps, though stumps aren't classically a thing without sending a woodcutter up a Z to chop at Z+1 level, right?), and I was previously (except that I thought I'd only be lurking, so refrained) going to suggest a 'ground shade' of overlying Z-obstructions. If the graphics engine could manage it, more diffuse the higher the shadow-casting Z was (adding loads of necessary computational power, but then you're already stressing one core of you CPU with all the physics, you might as well ask the other core(s) to pull their weight, right?
).
And one can continue the above ideas with half-transparent/'hovering and bobbing' overlays to put hints over other things (e.g. your icon(s) indicating stockpile types, with or without any goods in them to show explicitly, allowing a food stockpile with left-over logs in it to show both intention and reality).
But this is beyond my paygrade (especially if this
is now a financially remunerable effort, congrats!) so probably not a set of ideas to take too seriously. But food for thought, or at least a quick snack to keep you going before your late lunch, right?