21.078 Info PrototypeList.cpp:80: collision-layer counts:
21.078 Info PrototypeList.cpp:82: Constructron-Continued: 1
21.078 Info PrototypeList.cpp:82: Mining_Drones_Remastered: 1
21.078 Info PrototypeList.cpp:82: RenaiTransportation: 1
21.078 Info PrototypeList.cpp:82: alien-biomes: 1
21.078 Info PrototypeList.cpp:82: base: 23
21.078 Info PrototypeList.cpp:82: the-one-mod-with-underground-bits: 34
21.121 Error ModManager.cpp:1751: Reached id limit for collision-layer. The game can't contain more than 55 instances of this prototype due to hardcoded limits of the engine. See the log file for more detail.

update: it's because of your attempt at compat with NPT that it's running out of layers

The only reason it has so many collision layers is because you have too many pipe mods installed. Either disable a few, or get rid of NPT, or AUP. I won't be looking into this issue for the time being.

fair, i realised that myself about 10 minutes ago