I have seen situations where they have built up manholes despite interference from utilities. Usually it involved "cutting" a side of the manhole structure square with the sidewall of the excavation that contained the interfering utility (as opposed to a full round structure)
For example, we had to connect to a 42-inch brick sewer by building a manhole structure. The structure's total circumference interfered with a 24-inch watermain. They poured the bottom slab, brought the structure up with manhole block, and poured the sidewall between the 24-inch water and the 42-inch sewer. I've also seen them build up sidewalls with manhole block as well.
Typically, if you run this stuff by the City prior to installation, they don't have a problem with it as long as the structure is properly mudded both inside and out.