I've also done a fair bit of Malzahar jungle, and I agree with some of the points you made here and disagree with others.
I personally max RQWE because E doesn't really matter in the jungle.
In lane, you max E first for the extra damage for wave clear and the extra mana refund. In the jungle, the mana refund doesn't matter because it always restores less than its cost, the damage isn't as good as the damage on Q, increasing the mana cost on E is much worse than increasing the mana cost on Q, and the cooldown reduction doesn't always matter because you won't get a second E when clearing a camp or in a gank regardless of how long the cooldown is, and in early teamfights it might not matter too much.
Maxing Q in the jungle, on the other hand, does a lot of different things:
-it gives him similar/faster clear speeds to E max
-it gives him better ganks than E max (weaker ganks than W max because of W's damage)
-it makes Runeglaive much safer to utilize in early game teamfights (anyone needs to use Runeglaive passive in order to use it at all)
-it gives jungle Malzahar unique strengths over lane Malzahar; lane Malzahar needs to max E first because of his mana costs, but jungle Malzahar has Runeglaive to solve his mana problems so he can afford to max whatever he wants, and Q gives him a 3 second silence at level 9
The only advantage E has over Q max is that it makes it easier to take Scuttle Crab (which isn't much of a problem after you get Runeglaive) and that you don't need to try and hit with Q, but the reward for landing Q is significantly greater than using E on someone.
I also go
instead of
because I found that sustain isn't a big issue on Malzhar due to voidling tanking, and you can kind of get away with not having the mana sustain on Ranger's Trailblazer on the first few clears despite not getting the mana sustain on Machete, and mana isn't an issue after getting Runeglaive. Malzahar having that slow earlier than getting Rylai's is huge.