We built an extension over the sewer line running about 3 meters behind our back door. Issues were:
You have to apply to Thames water for permission with drawings etc showing how you will prevent any additional weight being placed onto the sewer, and pay a fee. It takes time so get it done before setting a build date.
You need a manhole where your waste pipe enters the sewer, so that you can clear blockages. So you cant just get rid of one that is in the way
You cant have an internal manhole, so you need to move it if it is in the way. This means backfilling and then digging/building another one further out, and re routing the sewer and your waste pipe to it. Not the biggest job but adds to costs obviously.
If it affects your neighbours you will need to speak with them, not least because they wont be able to use the loo while its being re-routed.
Any foundations that sit across the sewer have to be as deep as the sewer - so in our case the sewer was a full 2 m down, and we have to have 2m foundations, even though this was well in excess of what was needed for the building itself. This is to stop weight being placed onto the sewer.
You need to bridge the sewer line with load bearing joist.
There are minimum distances between the building itself and any manhole, that said, Thames water were reasonably flexible around this.
In the end to save money and hassle we designed the extension to step around the existing manhole, which worked fine for us - so it is now directly outside the back door.
Thna,mes water have a guide on their website to what you ned to consider in the design and have to put in your application form.
Ive attached the drawings we sent to Thames water if it helps