Module icons from Bob's Assembly overlap with the icon from this mod. Not a big problem because you can turn the module icons off.

Yup. Right now, the mod is using the same relative offset for the lights on all machines. It seems to be working acceptably for the vanilla version machines, but some of the other mods are a little tricky. I may start hand-crafting the positions some time in the future, but it is not on the immediate todo-list.

Just look at forum thread. I've left there new version, where you can toggle signals visible or hidden with hot key. It solves all overlapping problems. And also I've modified method of positioning of signals, so now they're been placed right in the bottom-center of any machines, even small (assembly zero, 1x1) or big (bucket wheel excavator, 7x7), even if machine is non-symmetrical (selection box is, for example, {{-1, -3} {2, 4}}). But I'm not GitHub user so you should contribute it yourself. My code is WTFPL.