Matt, in Stake Here mode, North/East, CTT, DTT, etc whiteboxes should not be filled, it is correct behavior - when you stake along a line, onle left/right indication makes sense. Also, each time you press "Stake Now" in CoGO Divide, mode is automatically switched to Stake Here (as it was requested some time ago), so the only way is going to Prepare Stake screen and switching mode back.
On the other hand: there indeed is a bug with stake step ignored when creating an alignment from the Divide screen - thank for finding it. Also, the alignment will always have starting and ending points, so it doesn't suit for this specific task of staking a single point. I wouldn't use alignments or line staking for this task, just conventional CoGo tools. Also, choosing created point for staking may be faster in stake "from map" mode, avoiding searching for point in the list.