You argue based on realism in all your points. However if you want me to change something, it should be something that improves gameplay, or is more realistic but has no negative effect on gameplay.
By the way, the question about accuracy has popped up more than once. And I think with the renaming of the treaded units to artillery units, it has become pretty clear that their purpose is, indeed, attacking human fortifications.
However, I feel that base bombarding is much more fundamental and important than collateral damage - I suspect that's also why you allow access to accuracy rather early. It is a mechanism that makes base assault viable - whereas collateral damage is more "stack busting", which is pretty important too, but not as fundamental in a strategic sense.
So, from my point of view, making base bombardment inherent of artillery and cruiser units would make their role and niche much clearer (that would help new players as well).
Additionally, making collateral damage a special ability (I'd call it "Flechette Ordnance" or "Flechette Guns", as a small homage to the Flechette Defence System, plus real flechette ammunition does collateral damage) allows you to restrict the range II spec ab - since you can only get two, you have to choose between range I + collateral and range I + II, because the ability to do collateral damage to an adjacent square (range I + collateral) is very good already, having it over two squares makes a properly upgraded artillery unit almost equivalent to a bunker for weakening enemies.
Plus, collateral damage is a much "flashier" special ability than base bombardment and could be opened up for other units as well (cruisers, aircraft and perhaps flamethrowers?) - and you could tie barrage-like promos to it, as follow-up.
Anyway, even if you don't want to go with that, I think that the "accuracy" spec ab should be renamed to "siege mortar" or something along these lines to make clear what it's used for.
Cheers, LT.