IME, it depends on what the stores focus is. I've not done much RPG at FLGS, but I have done a lot of board gaming. Most stores seem to focus on CCGs as their primary revenue, as they are by far the most lucrative product. For them, unless there's a CCG event where they need the space, they don't care much if the tables are used for other activities, as they pickup some revenue from selling snacks/drinks. I know of one store that focuses on miniature gaming, and they get a large chunk of extra revenue by renting out storage lockers (which is really convenient for any type of gaming, really). Another store focuses almost entirely on RPG and board games, but they supplement it with a video game center with recliners and big screen TVs (they don't sell video games, so I think it's strange). If a store wanted to charge for table space, we'd certainly find somewhere else to play.
The biggest issue with micro-transactions for gaming bonuses is getting everyone to agree to accept them. As a DM, if the requirement to run a game at the store was to allow them, I'd probably do so, but it would reduce my seriousness of this game. The store could also try the same thing for board games, allowing a re-roll, bonus resource, or card draw, but I don't think most board gamers would even consider allowing such a thing (I'd view it as cheating).
