I would think that if Scotty can automate the damaged Enterprise, albeit with mixed success, in the 23rd century, then surely Starfleet could figure out a way to automate a Miranda with some degree of success in the 24th.
That said, Scotty does note in TSFS "I didn't expect to take 'er into combat, you know..." Now, what does he mean? "I should have done a more thorough job if we were going to fight" or "Automation always fails in a fight"? And either way, why would we think it would be the same in the 24th century?
From the Lantree and Brattain we know at least that it is possible to automate them for non-combat missions.
Regarding Miranda outfitting, indeed we do not canonically know what the first ship to use this configuration looked like. What we do know is that it seems to be very modular and adaptable. Personally, I assume the roll bar to be standard equipment, but perhaps easily removable for different mission types. Other configurations would be variants rather than refits - consider the Nebula class variants.
There is something to Timo's notion of the old gals not being able to handle it anymore - most of the ones we saw in the Dominion War (with rollbar) appeared to have higher registries, implying newer vessels. Then again, so does the Saratoga, which had no rollbar, but did have modern control surfaces in her bridge, civilians aboard, and escape pods in the shuttlebays.