Thanks, that save was exactly what I needed.
Worth flagging first: the save says Factorio 2.0.77, with this mod at 2.0.14. The 2.1.x releases only go to Factorio 2.1, so nothing I said above about 2.1.2 or 2.1.3 ever reached you. If you still think you're using 2.1.2, please give me more information, but I've at least solved the problem in 2.0.14.
The mod was reading "this ground has a cover tile on record" as "this ground needs paving". It does not: that record is a paving choice, and the game keeps one per force for each kind of ground. Something in your game has asphalt on record for ordinary ground, so every connector got an asphalt tile ghost under it, and the connector itself was downgraded to a ghost instead of the pipe you had just paid for. Nothing Pyanodons specific about it, any force with a tile on record would see the same thing.
Fixed for 2.0.15: a cover tile is only laid where the ground would really stop a pipe sitting there, water and the like. I brought the two related fixes over from the 2.1 line as well, so a cover the game would never let you build, asphalt on water for instance, now falls back to one it will, or to leaving the gap alone.
Checked against your mod list on Factorio 2.0.77, every tile it puts in the game, with and without a cover tile on record: 62 tiles, and nothing paved that a pipe can sit on. The same run before the fix paved 66 of them.
Please let me know if this solves the problem for you, in SP and/or MP.