Vinn, thanks for all the information.
I have spoke to a neighbour who knew about the concrete cap. As suspected, it was some sort of sewage pipe; a big one apparently, 8 inches in diameter. The other houses on the row didn't have one, however. Not sure why that is. Apparently, the previous owner had it investigated (internal camera) and they were satisfied it was not in use so it was removed and capped off with the offending concrete plug. Mystery solved. I think I'll leave it where it is, though. Already got a list of jobs as long as my arm.
To answer your other questions, there is no gully in the yard, but there is a drain at the bottom, and yard slopes down to it. I think you are right in stating that the WC position is not original; I believe the previous owner altered the size and layout of the bathroom, so the position of the soil pipe was moved. The soil pipe is plastic and relatively new, supporting that. Also, we were made aware of the leaning chimneys when we had the survey, and it's on the to-do list.
Thanks everyone for your help.