During prayers conducted by the Chaplain, the Chaplain, not the Commander, determines whether to re-move covers or remain covered. Most Chaplains prefer to uncover, but there are some who remain covered. The Post just needs to follow their lead. And just a small side item, when uncovered for a prayer, the cover is held over the heart with the Cross of Malta showing.
Speaking of covers, when attending any VFW meeting, only VFW covers are permitted. If you forgot yours, being uncovered is fine. What isn’t allowed are baseball hats, sombreros, cowboy hats, or any other head-gear, not even Seahawks caps.