Well none the less, some faction specific traits would go a long way to making the factions unique. This being more an issue between CSM and SM of course. Having some unification isn't a bad thing.

I'm not sure whether we should expect factional differences in the game at launch (such as Chapter Tactics), but maybe some time after.

Probably it had been mentioned somewhere before but I expect Iron Warriors to have some significant heavy weapons buffs\bonuses like: higher dmg against vehicles\encampments, quicker way of obtaining some heavy weapons. Also faster time of retaking enemy strong holds or less dmg taken while defending our own bases. All these ofc are in accordance with the lore.

Would like to see Marks of Chaos instituted what better than offering benediction to a dark god and receiving their blessing.

What Viehmanns is saying is what i would say. Mutations are a good consideration or at least something similar for Iron Warriors and Night Lords, but if you want to go further down one branch of the tree then we may see dedication to certain gods, granting marks of Chaos, further varying and adding new legions that were not implemented (or at least playing in their style, don't get confused and think I am requesting new legions). You might even see clans popping up dedicated to certain gods through this playstyle, but it could be a very interesting way to go.

Instead of chaos in general special abilities how about a sub faction ability per sub faction. I know the Night Lords want the banshee scream.

well for the chaos god sides Khornes ability would be let the galaxy burn* balls of fire* tzeentch would be Bring forth the warp*summons deamons to aid you* Nurgles would be fly swarm*as the name says but causes damage or heals friendlies Slaanesh would be This quite offends SLAANESH!* Cause massive ground tremors stunning or knocking back enemies.