Who said this was all exclusively about drafted units? Summons are just as relevant for the discussion.
The example you took, from page 41 is built around the current state of the game. It is geared for stacking enchantments and researching.
The build would change if limits were introduced. I don't know why I have to explain this, it should be fairly obvious as a result.
I would adapt all of my builds to not go beyond the limit and pick up extra units or specific spells as far as general planning goes.
And during the actual game I would pivot into another tome if I needed a specific counter enchantment to beat my opponent.
Right now these kinds of dynamic choices don't exist because you can just stack everything without any engaging gameplay at all.
Well, as it turns out, an instant death ability that is based on missing HP is weaker than actual death by stacking damage enchantments.
How someone thinks the problem should be addressed is open to some discussion, but the problem is very simply that death is the strongest CC.
Got a disrupt? Cool, but if the unit was dead it would do less damage than without enchantments, so stacking more damage is more effective.
Got stuns/blinds/etc? Same problem. It would do less damage over an even longer period if you incapacitated it by killing it.
It becomes solely a battle of survival vs damage output, which basically has three possible states.
1. Durability is so high damage output can't kill units before dying themselves, so you can only compete with different durable units
2. Durability and damage are about even, which has exactly the same effect over time as just removing ALL buffs to either (I am not saying this is a good idea, I'm saying this is the best case scenario among three awful options)
3. Damage is so high that more durable units still die immediately, so you can only compete with other output units (we are here)
Instant death is another example of this, because using a unit's turn on possible instant death is only valuable if damage isn't high enough to cause instant death with regular attacks... which it is.
I suspect this is outside the scope of a rework at this point, although I'd be delighted to be wrong, but the only way to fix the core problem (stacking damage vs stacking durability is either pointless or has a clear winner and the other is nonviable) is to remove simple stat buffs from both enchantments and transformations. No unconditional damage, defense or resistance buffs, only more interesting or situational effects, and the problem is gone. I'd still favor an enchantment cap (and a transformation cap), but all it actually needs is this and the problem we're actually talking about is gone, even if I think unlimited stacking of both is bad separate to it.