It could be said that, where pipes cross, it's preferable to dig a little concrete out and cross "under" the pipework.
Easy for me to say here. There may be a good reason for the way they've done it.... apart from making life easier for them.
Anyway, no matter. Yes, cut the insulation as necessary to channel the pipework into it.
Unlikely as it may seem, it's standard practice to lay concrete or screed over insulation. When set, screed acts as a giant slab bearing on the whole floor. Its integrity is such that the load is distributed over the whole area.
If you divided the load by the floor area you'd find that the load per square inch/ sq. metre etc will be minimal.