You may need to apply Superior Designs decision on your planet before you can start building enigmatic tech buildings.

I've already done that. I can't build the second level of it for some reason

Then as per usual. Check if you meet all the requirements. If yes - check for mod conflicts which may break the upgrade.

If you have ! Better Performance & Utilities or ! Production Revolution then disable them. I had same problem which these mods cause them for me.

I found the issue. The building has a Population requirement of 20 to build and does not take into account the manpower stat of PR. If you want this problem to go away you have to convert manpower to pops to have at least 20 of them or go into the mod files and edit it to reduce or remove to pop requirement. pathway to find the file is, Steam\steamapps\workshop\content\281990\1419304439\common\buildings\acot_01_alpha_buildings.txt

Edit: tried it, event removed the pop requirement entirely. didn't do anything.