It looks like the icons are incorrect in the latest update. They still have tint=transparent in the code, but you've renamed the transparent variable to underwater_tint, so they aren't correctly underwaterified :)

Thanks for the mod btw - I have now integrated the bits that I wanted directly into Freight Forwarding, so it isn't actually depending on this one anymore. But the inspiration was very helpful :) I realised that I didn't need/want the underwater-pipe-to-grounds, just the basic pipe. And I was able to remove the '-placer' entities and just do it all with collision layers.