Black glass is something that could be tweaked perhaps.
The new FTL update has arrived and no doubt discussions will arise around designs and functionality.
While it is all welcome, of course, do note the normal maps are placeholders, the Warpgate modules are waiting for 24 way orientation to allow a proper tiling pattern and until a new monitor arrives the colour values are considered "in limbo".
Those wanting a completely transparent warp gate, please follow these simple steps:
Open the T002.png file in any image editor capable of handling transparency.
Find the warp gate module texture and delete it (all 6 tiles), leaving only transparency, then save.
Open the Block Editor and under the Stations tab, select the warp gate module and toggle the options "Blended".
(potentially, you could set the block to non physical in the block editor too, but i'm not sure if it would conflict with the mechanics)