When mousing over an underground pipe and walking, because the selection box isn't the full size of the pipe, the pipe overlay flickers on and off.

Is this intentional? required? as it seems to select the underground over the regular pipe, like it is 'higher', i'm unsure if this is the only way to make it selectable over the normal above ground pipe

Ah yes that's unintentional, an earlier implementation had the individual underground pipes selectable but they no longer need to be so. I'll hide them in the next release.

Dammit wrong mod. Yes this is intentional and required, as otherwise you would not be able to deconstruct them. They are also smaller than normal because you need to be able to select the entities under them. There's no way to get them optionally selectable at runtime, so they have a higher selection priority but a smaller selection box to compensate.