Here's the answer, thanks to Brother-In-Law Tom Kuhfeld:
In order to properly pave over manholes etc, they take the casting off and pave over everything. If they didn't do this, the screed on the paver would catch on them. Before the last coat of asphalt, they dig up the manhole and replace the castings to the proper finished level and patch around them. When the last layer is done the mix is laid down a little high to account for compaction when they roll it, so they aren't then an issue for the screed.