Can't reproduce any of the following: the positions bug on (4) Twilight Heat, the Eradicator affecting units aboveitself, or the Infantry Only aircraft bug. Aircraft are all locked with a TechLevel=11 setting in Infantry Only mode, and I unlocked none when I captured the Tech Airfield on (8) Arctic Circle. Are you sure you're playing on version 3.3.5 without any external modifications? I need more details on exact subfactions and units used.
The advanced Epsilon defenses built by the AI are clones of the originals,with TechLevel=-1, so TechLevel settings doesn't affect them. Currently there's no workaround for this, it's a fix for AI not building defenses that require an upgrade rather than a proper building.
Shadow Tanks can be built if you capture a Pandora Hub with Psychplug even if you don't have the Epsilon War Factory, it's an alternate prerequisite kept as a workaround for another issue.
Epsilon Elites are blocked for the others, you must be explicitly PsiCorps to be able to train them, otherwise you get the Adepts.