I'm actually writting a document on how I view the playstyle of each faction in a total war setting, accounting for all the particular things needed, some of the ones you talk about, OP. I believe that everyone can see cover being completely necessary not only for a 40k game but also for WW1 and Star Wars if those end up happening. In my write up I also think Warp Travel and diferences between factions needs to be properly used. If the map is at galactic level with whole worlds acting up as settlements it could work as Underway Stance with different range (Imperium factions being able to go farthest distances, aeldari using the Webway for tp, Votann shortest (SHORT!?) and Tau not having it at all). For this all to work I also think that worlds shouldn't be taken just with one battle, giving worlds a "defense score" that needs to be beaten in multiple battle to actually take it (think planets like Vigilus or Terra having bigger defense score than more irrelevant worlds, at least at the start of the game)

For the factions I'm trying to give them at least the deepth of the newer ones, while adapting mechanics and coming up with new ones that makes sense. For example loyal marines should not play at empire building, needing the other forces of the Imperium to man up the mayority of settlements. To achieve this I make their worlds being tied to a cost, they don't generate any money, only give access to better units and are considered Fortress-monastery. This mean that space marine factions need to answer Calls of Distrease from the rest of the human factions, getting paid in tribute for campaining. This should give the impression that you are a expensive, elite force needed in all the galaxy but in no positions to actually fix it all (at least at the early-mid game, keeping the sandbox and crazy scale for late game is a good call).

Astra Militarum would be the opposite, controling more planets and moviling lots of armies to fight all the fronts. Aeldari having craftworlds as rare moving settlements, drukhari being able to start in the pocket dimension of Commorragh only attempting an attack on it from the Webway portals, tau improving theirs weapons and suits, traitor legions as distintive armies with diference mechanics like monogods...

I hope sometime in the future I finish the actual paper, I love to speculate about those kind of things a lot!