Hmm, an interesting issue an I agree, this is very unusual. One can only speculate as to how this happened, but the most likely reason is that the land drains for the whole estate were established first with the groundworks, long before the developers legal chaps worked out exactly where to put the marker fences in place that determined the land ownership. I had a similar but less controversial issue once where my soakaway (5 metres away from my property) was in a neighbour's garden.
If in England & Wales you may be able to benefit from the legislation enacted on 1 July 2011 whereby the responsibility for maintenance of private sewers and lateral drains was transferred to the water company from 1 October 2011. Details here: -
http://www.water.org....er/about-the-transfer
This legislation was not enacted to cover the situation you describe - it was intended to cover where other people's sewers run through your land TO WHICH YOUR OWN SEWAGE also flows.
As far as I can see, you have absolutely no interest in the offending sewer / manhole cover, indeed it shouldn't be on your land. As such the water company should have an easement for it, which I'll bet they don't have - check the restrictions detailed in your Land Title at the Land Registry. If it doesn't appear, that is perhaps your best negotiating lever.
You are correct that the builders are unlikely to want to know after 13 years.
The situation with the estate developers is that that they enter into a legal contract with the water utility / local authority to construct the sewers, roads, street lighting to a specific standard that then gets legally transferred in terms of future maintenance responsibility when the estate is finished. You could try pointing that out to the water company - it is only they that could get recourse from the builders.
But my starting point would be to suggest to the water company that it is their responsibility - the technical stuff is that it is contained in section 42 of the Flood & Water Management Act 2010.