Just did this early this month. These were the last holes I drilled on the side skin before doing the big dis-assembly. No particular reason it was last, probably just because I hadn't loaded my #30 bit in a while and this is what was left to do. You should be able to drill that whenever you want after the skins are on and everything is square. I do know that I didn't rivet the side seat ribs to the bottom skin until much later (this past Saturday).
On a side note, the massive dis-assembly of the entire center/forward section is the most demotivating part of the build so far. Seems like such a big step backwards - it isn't of course. Eventually you get to put it back together for good though.