Not over thinking at all...definitely too much head space especially if the SG is at 1.000 or less. If it is still fermenting you will have a protective layer of CO2 for a bit. As far as topping up I do not like to use water because it simply dilutes everything. Not sure what your base is but if you have more of the same and can mimic the original gravity of your original must you will have a perfect topping up liquid. And then there are the lead-free glass marbles, or SS shot, 3# will displace one liter.
Motto: quel che sara sara