Is there a macro command for this...

[Callinon]

I didn't lose uptime with my old setup actually. Just pressed the macro between the GCD for kaiten with no clipping. Unless there's some funky artificial lag macros cause that I'm unaware of.

So is there really 0 macro commands that could somehow eliminate the risk of excessive kaiten use? Like a command that says "wait 3 seconds before using X again"? I'm not overreacting when I say having to change muscle memory for this change is going to suck otherwise.

There really isn't.

You can issue a /wait command or end a command with a <wait> tag, but those will insert a delay before absolutely anything else will happen. Inserting a delay that will only prevent one thing from happening isn't possible with this macro system.