What you’ll need to do is make a custom tophak for your server that has the 2da merges in it. You don’t need to alter the contents of CEP or Q core packages as you can specify which content to use in your merged 2da files.
When setting up HAKs for your server, I would keep CEP on top of Q. Then run the conflict checker (its located where you add haks to a module). Then you’ll see what CEP content overwrites Q content, as well as what each package overwrites from the vanilla content.
By keeping the CEP and Q core haks intact, your players will only need to download any server specific haks you make so it won’t be much of a pain - assuming they already have CEP and Q installed on their systems.
The Q haks are also designed to work independently of each other as opposed to the CEP haks which require all their haks to work. Thus, if you want the Q placeables and creatures for example, you can just link in q_creatures and q_placeables and be done with it.
As for Q being “high-poly”, they’re more of a mid-poly count and have been thoroughly tested throughout the years of development. Granted, I didn’t test them widely with EE before I released Qv3.0 and Qv3.1, but I never experienced any issues due to polycount on my old computer under v1.69. I also did quite a bit of benchmarking with the Q TNO extension and the other tilesets in the q_!tilesets hak and was able to maintain fps in the 60-70 range under typical encounter loads in single-player. The only complaint about fps and lag I’ve heard was actually traced back to improper handling of the v1.69 horses.