Can use FTL Modifiers - when you check this does it blacklist me from using ctrl-1 ctrl/shift 1 or whatever as an another isboxer game helper macro?

For Example Focus {FTL} game helper macro has all check boxes "allow extra modifiers" and "can use modifiers" checked off. If can use FTL~ is checked off why need to check off allow extra modifiers?
FTL is mutually exclusive from the optional modifiers. You aren't looking for FTL here, you're just wanting the optional modifiers.

For the macro you have pasted, just check the left ctrl, shift and alt boxes in the WoW Macro Library for these optional modifiers. (Read your macro... mod:ctrl, mod:alt, mod:shift. check a box for each mod:???). You will want to assign a Key Combination that does not have any modifiers in it (that would conflict with your "optional" ones). For example, if you put Ctrl+F1 here, then Ctrl is no longer "optional" because you're forcing it to always be there. So anyway, I'll call it F1 for the rest of this example.

Then, when you use a Named WoW Macro Action to activate your example macro (from the WoW Macro Library which has ALLOW ctrl,shift,alt checked), you can check the Ctrl box in order to send Ctrl+F1 instead of just F1. Check both Ctrl and Shift o send Ctrl+Shift+F1, and so on.

Hope this clears it up for you.