BOB is used quite a bit in team games as a way of sharing the view of the map between teammate turns, that's probably the largest use of it. There are times when I use it to check an attack path, if I can't see clearly on the screen -- some maps are more challenging than others to see the paths, and there are times it comes in handy when learning a map you're not familiar with. If only people who knew a map played them, we'd never have maps clear the Beta phase as nobody would be playing games on them.
That aside, I think I may have stumbled on to a "workaround" ... changing the BOB setting to move the chat to the top seems to have repositioned the popups so they don't interfere with the clickable maps functionality. It's taking a little getting used to, but I think I could get accustomed to having the chat as the first thing I see on the game/map page. Seems to be working in my regular games and in the tournament games.
Highest rank/rating -- Major / 2225 points -- May15, 2014
Kuma's GC Qualifier: City Mogul
Jules Verne Contest - Team Finals
The Great Community Map Project: Tournament Five
Serbia's NFL 2013 Poly Trip