Unpopular opinion incoming...
From my own angle, and the way I see things now. The OmniFactory should be left to slumber, for it is no longer needed. The new mechanics in 0.8 make both acquiring new ships and not losing existing ones far more tenable and does so in balanced manners. While the OmniFactory is just a big giant cheat, that breaks the game mechanically and lore wise, removing all scarcity.
I understand why folks like it, but it broke the game even in old versions, and it really would now! Think about it objectively, truly isn't it an obsolete thing these days? You can make bolder decisions now, without worrying as much about losing your stuff. Adding the OmniFactory back to modern versions of the game is hilariously unwise. Perhaps let it sleep, and wait for vanilla manufacturing to be added. In the mean time, salvaging and new D ship mechanics has your back covered.