I can help
The engineer should be made aware of what services are in place, but he would not be finding this out on his own. This would be provided to him.
This could come from the architect or the civil engineer, it really depends how the contract is written and what is in each person's scopes.
For a house, though, I don't think it would make much of a difference. You would not really be building a house on deep foundations. It would be either a mat foundation or strip footings.
With either one, getting utilities through, or under, the foundation is not really a problem.
Unless the utilities are existing, then it's another ballgame.
And someone needs to figure that out, but it's not the structural engineer.
If you could rate my answer, I would appreciate it. I'll be happy to answer additional questions on the topic.
At least it sounds like you have a direction forward. Even if it's an expensive direction, hopefully it will get you out from under the situation.
Underpinning is an expensive process. Adding piles and grade beams is also an expensive process. They are options out of a difficult situation, but they do cost quite a bit.
I always recommend engaging a professional (not a contractor) for your own peace of mind. An engineer has no vested interest in having you pay more than necessary for the work.
I don't do anything with sewers, but I'm sure a civil or mechanical engineer could help you.
The SE would typically design the foundations based on recommendations from a geotechnical engineer for the foundation type. The SE generally has a good idea of what type of foundation is needed, and is in line with the geotechnical recommendations. The SE can't make assumptions about what is underground. He is relying on others who have knowledge of this to alert him. It would generally be the responsibility of the prime contract (usually the architect) to find out himself or engage someone to find out.
In the US, you're supposed to call the utilities before any digging happens to find out where things are. If you don't do it, you really own whatever problems come up.
I would expect the prime contract to take the lead on this.
He dropped the ball on that one.