Currently to get water we have to make an Offshore Pump and place it at the edge of a body of water.
My idea/suggestion is this. Get rid of the Offshore Pump and have the boiler act as one when placed as shown in the picture. As in at the edge of a body of water.
The idea for pipes has been covered in many suggestions already.
Either add a recipe for covered pipes (catwalks) that is pretty much a pipe plus an iron plate. Would only work for regular pipes.
Or add a researchable upgrade for regular pipes that when researched sinks them into the ground. (Yes I know there's a mod that does this already. Not sure if its still useable though.)