The purpose of the agreement is to make sure the pipe can still be maintained and will not be damaged by the new foundations. Building over a defective pipe without repairing it first is the worst possible outcome — you have entombed a fault.
Practically, you should always CCTV survey a run before building over it. Repairing a defect while access is open costs a fraction of dealing with it after the extension is up.
Missing build-over agreements surface at sale and can delay or derail a transaction. Regularisation after the fact is possible but slower and more expensive.