It's just an opaque way of doing it with a poor ui tacked on
I'm not going to disagree with that sentiment. It could be better presented and explained, and that would help in a lot of ways.
a division made of 6 marine, 6 mountaineer and 3 artillery battalions
I get the point you want to make is that 12 > 6, which is perfectly true... However, that specific division would be a wierd, unworkable beast IRL (which is what the game purports to simulate, after all) since Marine and Alpine units have very little in common, and anyone who ever designs such a monstrosity deserves to end up with crappy units

Similarly, some of the other hypothetical divisions you quote would also be wierd hybrid monsters that have absolutely zero RL parallels, but I take your general point. As the player, you are free to construct any illogical, counter-intuitive, unworkable-IRL design you like
and not be massively penalised for it though, which actually you probably should be. There does seem to be some unstated assumptions built into the Div template designer like "noone will ever be dumb enough to combine multiple SF Batt. types in a single division template" which can produce these wierd effects, which is part of the problem here. I'm actually OK with that division being Arty, since it would properly punish the player for violating basic tenets of unit organisation. As an SF unit, it would be neither fish nor fowl, and should therefore get none of the benefits of being either. Maybe they shouldn't get the Arty guy bonus either, but if you refuse to conform to RL practice, you can't really complain too much about your Div design bonuses not making sense. What Div type do you think the game should rate the following as :
2 x Marines, 2 x Paras, 2 x Mountain, 2 x Mech Inf, 2 x Mot Inf, 2 x Mot RA, 4 x Cav, 4 x Arty, 1 x SH Arm, 1 x HSPG, 1 x LTD, 1 x Mod SPAA, 1 x M Arm.
Technically, that is a valid Division... but what a mess. What is it for? What kind of battle is it intended to fight? Why does it deserve any bonus whatsoever, from any source?
You do see something of this effect with paras, since any Div containing ANY non-Para Battn cannot be dropped (although I guarantee you will see Air Landing Div types in a future DLC, which allow straight leg inf, airmobile arty and airmobile light tanks to be attached to Para Battns, and be droppable, so long as you have the glider capacity - when gliders get introduced. And the airmobile versions of LTs and arty, presumably on an extra research tab like the TD / SPG / SPAA armour variants in the current version)
Anyway, whilst all that is a bit removed from the original topic, this is a bit of a wall of text already, and I've said most of what I wanted to say, I think. Yes, there is a bit of gameyness in it, and possibly the whole thing needs a bit of polish, and definitely more transparency, but I don't think it's all that bad as it stands