The issue described above is easily fixable by using Redrawn Space Connections. However, I have another bug with Any Planet Start compatibility.
This mod tries to detect whether Gleba has been deleted by whether the Gleba planet discovery technology is hidden. However, this is also hidden by the Any Planet Start mod if the player is starting on Gleba. This mod can therefore make the game unplayable as it changes the bioflux recipe to require materials not found on Gleba even though the player is starting the game on Gleba.