How would you expect to ever make a professional looking RTS game if the selection box has to be tile-based?
Here's a professional looking RTS:

To make a game like that with BYOND, the part that concerns you most is how we'd create the selection boxes? Seriously?
BYOND games don't look professional and they don't need to. People will overlook these kinds of details to play a fun game. They play games with retro-looking graphics (and I don't just mean the BYOND games with retro graphics, there are lots of popular games) and they play BYOND games even though most only run at 10 frames per second. If you make an awesome RTS and the only bad thing about it is the tile-based selection boxes, I guarantee that people will still play it.
Things just aren't that easy when trying to make an RTS. You have to spend more than half of the development time just getting the interface to work, before you can even start testing the other functions with the controls.
BYOND provides what you're calling "RPG controls" because those are simple. BYOND doesn't provide controls for a platformer, board game, or racing game. You can easily create these features and provide them as a library. It'd be nice to be able to provide people with these features, but it doesn't have to be something that comes directly from the BYOND staff.
I kind of like Tom's idea of there being a specific client-side notation for a mouse-drag triggered box. I assume that would be about as efficient as icons moving through frames or states. Perhaps this exception could be integrated as a kind of skin layout option for the map. Of course, this would probably be purely visual, so the actual detecting of mobs would be a whole other issue.
I think BYOND has put the cart before the horse by providing isometric view before draggable boxes even get properly implemented. So, BYOND developers have had to figure out workarounds to push the cart along, before they could even get started on a real RTS project, which is one of the reasons why so few exist.
BYOND practically hands you the RPG controls right from the start. All you do is create a mob, and boom, you can instantly move it around with the arrow keys. Things just aren't that easy when trying to make an RTS. You have to spend more than half of the development time just getting the interface to work, before you can even start testing the other functions with the controls. For RPGs, the arrow keys are the most basic interface function, but for RTSs, selection boxes are the most basic. That's why it would make sense to basically provide this function for developers right from the start.