In the 2.5 build there is 6 extra wires that are potted through the end cap. What are those for?
for future devices or options
so I don't need to lose sleep over them?
Nope! You can use them later for other devises if you elect too. In the mean time, if you're not using them, I recommend covering the loose ends with hot glue so water doesn't travel down the wires between the insulation and copper.
All the best!