I don’t know Axolotl Plugin in detail, but it seems you are using it wrong.
The lattice you are using divide the space in two infinite periodic volumes A and B… but the mesh itself is not a solid per se, but only a “limit surface” from volume A to volume B.
With SDF volume A will have positive values and B negative values.
When you make a solid boolean union/subtraction, you are adding or removing the set of values from your pipes to the lattice, but you can’t generate a “limit surface” with holes.
See it like mixing water with oil. Water is A (positive) and oil is B (negative).
The mesh, the limit surface Axolotl is generating, is the surface where water is in contact with oil.
Can ever exist a an interruption on the limit surface? Can exist a portion of non-contact between water and oil? (aka an hole in the mesh limit surface)
No.
First, generate your mesh, then, after, split and cut your mesh with other tools.
Isopod have a command that lets you use a field to split a mesh.
You can maybe exploit the engine and create a “bubble” of air between water and oil, where all the values would return a NaN value (so not positive and also not negative) … but this is bad practice and will return bad object or break the solver.