You don't have to use a named wow macro action, it's just a hotkey in the game. If you want to turn on Repeater and manually press whatever key combination you want, go for it. For example if you turn on Repeater and press Left Shift+F11, everyone should /follow the guy in slot 1. That's because follow is on F11, and the left shift modifier means slot 1 in the macro.

The reason I say that is because the answer is technically yes, you can change the modifiers, but you're not broadcasting your modifiers to the other windows unless you turn on Repeater or set up a Hotkey that uses the modifiers and specifically broadcasts it. So if you wanted to do that to a macro in the current window, all you'd have to do is turn on the Hold option for the Mapped Key that uses it, and you can hold extra modifiers. (Without the Hold option, only the modifiers specified by the Action are used!) For the other windows, you would have to broadcast the extra modifier.

It'd likely be cleanest to set up your extra Mapped Keys for each combination instead of trying to blanket-broadcast the modifiers (which might cause problems if you wanted to press alt+1 and have it just send 1)