The modifiers you set for your team, in the character set slot options...
Those are only going to apply to the three FTL mapped keys: FTL Target Me, FTL Assist Me, and FTL Follow Me.

Anytime you want your slaves to do something based on the main target, do it with a Do Mapped Key action.
If you want the slave to assist the main, use a FTL Assist Me, rather than a wow macro action.

You can use modifiers in your wow macro actions, irregardless of them being the same as or different from the modifiers used in the FTL actions.
There won't be a conflict.

If you had an action:
- Do Mapped Key > FTL Assist Me
- Wow Macro Action:
#show Nuke
/cast [nomod] Nuke
/cast [mod:ctrl] Insta-Nuke

The process will be:
- Backspace is pressed, with the correct FTL Modifiers so the game knows which character the others should assist.
- Now the Macro Action goes off... and this is separate from the FTL Action.
- So with or without control, the macro fires off as expected.