I'm glad you appreciated my feedback! :D
I feel like, if you're going to have a dedicated flag button, right click should be reserved for that, as changing it to some other button would mess with muscle memory too much. Alternatively, if you wanted to change how flags work (for example, the "tiered" flags concept), you could try using the scroll wheel for the flag mechanic? Right click a space to select it for flagging, scroll up or down to increment/decrement the number?
Then maybe left clicking a tiered flag auto-uses the lowest tier of regular ammo required, which could be disabled with a checkbox if you want the normal behavior of it using your selected ammo? Or maybe the ammo selection menu simply has a "smart select" option, and using that "ammo" automatically picks the correct ammo based on what number is on the flag? In that case, it would be worth deciding whether to have it use better or worse ammo if you don't have that exact tier, or if it should just pop up a message saying "no ammo" to tell the player they have to choose their desired ammo manually?
Could give the feeling that you right click and scroll to "aim" your weapon, and left click to "fire". For anyone without scroll wheels, they could just type the number with the keyboard. Number keys could also be used for the "Minecraft hotbar" idea, and a good way to prevent overlap would be to have the numbers enter numbers onto the selected flag tile, and you can hit enter to "confirm" the number, returning the number keys to their hotbar functionality while no "text field" is selected? Same for scroll wheel potentially being used for hotbar. Of course, you could add an option that disables the number typing entirely, for those who don't want to bother hitting enter before selecting their ammo, especially in cases where they actually have a scroll wheel. And a reverse option that enables number typing, but dedicates the scroll wheel to hotbar selection.
Or maybe you could also make it so right clicking to flag a tile, and then clicking one of the enemy "profiles" on the right, uses the selected enemy to determine the flag used? So if there's a 1 on a corner, you can right click the tile, click the level 1 enemy, and then a "1" flag appears? Would be slower than the other ideas, but very convenient for touchscreens, or people who prefer "intuitive" over "quick".
There's lots of ways you could go about making a new control scheme, but I'm a game design nerd, so I figured I'd give you some of my ideas. :P