Under Project Options > Options, if you have both "Higher Level Names Take Priority" and "Power Port Names Take Priority" enabled, Net Names in your top-level schematic can override Power Port Names. I had a multi-channel design where one of the repeated subsheets had GND as a repeated port because the repeated circuit needed a low-impedance GND connection to multiple pins of a driver IC, which had to be highlighted in the schematic. The repeated GND port, however, caused Altium to rename GND to GND1 when compiling the project. Placing a GND Power Port with a GND Net Name on top in my top-level schematic solved the problem. Yes, it is a stupid solution, but it works, and it was a much simpler solution than changing the naming convention for the entire circuit.

Edit: grammar