Whether you use pull-up or pull-down won't make that much of a difference in terms of operation, the main thing is syncing the microswitch to ensure it switches well before the opto switches. Personally I'd aim to have the microswitch switch when the opto is about quarter (1/8th of a turn) of the way into it's untriggered half of the disc. That way the switch should be firmly activated by the time the opto triggers.
If you use pull-down on the BOB, you need to ensure the microswitch closes when the opto is blocked (at near 0V), so that when the opto is unblocked, it pulls the BOB pin up to near 5V.
Or if you use pull-up on the BOB, you need to ensure the microswitch closes when the opto is unblocked (at 5V), so the opto can pull the BOB pin down when it becomes blocked.
Either way will work, it's just that the microswitch trigger point/adjustment may make one way easier than the other.