Actually only happens when the MLC is currently throwing an error. Two are added when there are no new lines at the end of the file and from then on only one is added. Same thing happens when I click save&close.

Right, added that in the last version, forgetting that gmatch will always return last empty string after final newline as the last "line".
Fixed in 0.0.29, though will bundle other things there first too.
Thanks for noticing, as I probably wouldn't, with my "paste and run" approach to code-editing with laggy in-game textboxes :)

Come to think of it, some significant part of lagginess is probably those fast gui signal updates and "undo" history action on each change, which saves stuff to globals, which then factorio should check in many ways, serialize, and then maybe even send over network to all other players - all for every single keypress in that textbox!

Come to think of it, some significant part of lagginess is probably ...

Yeah, it's so much faster and pleasant to work with without calling that rarely-needed undo-history handler, so guess I'll add a mod startup option to not use it.
One side-effect is that I'll probably never use it myself too, so if someone does like it, it's likely to get buggier over time that way.