Yes, you can drag the brush straight over the hole but a little extra care/dexterity with the brush can avoid any extra glue being left within the spoke hole at all.
It only becomes a minor problem when rim cement gets stuck in the spoke holes of rim with internal nipples.
Nothing a bit of petrol won't cure but most FMs don't like to see rim cement here, it's sticky and doesn't provide proper grip for spoke keys.
That said, the Veloplug idea to prevent cement from entering the rim is rather cute. Just remove them before the glue settles, clean them and that's that. Neat.