You could create most of your boxing macros as IS Boxer macros.
As in, made within the Toolkit.

That way, if you launch via Inner Space in the system tray, you have all the IS Boxer macros and such.
But if you launch via the Warcraft icon tied to launcher.exe or wow.exe, then you don't have those macros.

If you want all the macros to be in game.
Have IS Boxer interpret "1" (or whatever key you spam) to be two steps.
Step 1 sends Alt+Ctrl+[, and Step 2 sends something like Alt+Ctrl+].
Put the spam macros on a hidden bar, that has buttons key bound to those hotkeys.
It won't impact your boxing play, since you are spamming an easy key and isboxer is interpreting it as Hotkey A then Hotkey B, rather than your normal actual key.
Then put your one-box stuff on whatever keys you want.
If you launch with isboxer your spam key sends different things that if you launch with wow.exe