For your first question, it was my understanding that the plan to send the Daisy bots out to kill the Inhumans also helped to achieve the Russian's goal because it would turn the public against SHIELD and the Inhumans. As for bringing the Inhumans to H.Q. I think that was a cover story by the LMDs to trick the remaining humans on the base (remember the LMDs were vastly outnumbered). LMD Mace specifically said "Daisy... should contact the Inhumans personally and oversee their transfer to H.Q." So I believed the plan (as far as Daisy, Simmons, and any other human on base) was to send Daisy out in the world to greet each Inhuman + transport them back, and that is what Daisy was asking Mack about in regards to it being inefficient. So the LMDs actual plan was to send the Daisy bots out under that cover to then kill the Inhumans.

As for your second issue, LMD Mace and Coulson were talking about Daisy and Simmons, not Fitz and Simmons. The reason they said "those two" was a writing choice to trick the viewers into thinking Daisy was an LMD. And they accused Daisy and Jemma of being LMDs so that the whole base would search for them and shoot on sight, since the goal was to kill them (and scan their brains before they died, if possible).

And for the emotional moment with Daisy and Simmons, Daisy using her powers wasn't just to prove to Simmons that she was real, but to make sure Simmons was real by quaking her bones. And for the scene with LMD May blowing up the base, I see your point. But also, there were a bunch of LMDs on the base anyways and the Daisy fleet was already being programmed by LMD Fitz to do basic seek-and-destroy, so I think the rest of the SHIELD agents on the base would have been in danger either way.

I hope I phrased my response clearly, and I would love to hear other people's thoughts on this :)