I have no idea what to expect in terms of temp differences; it's immaterial, imo, and I wouldn't bother concering yourself with it.
As to whether the lower will reach done first it is hard to say. Proximity to the heat is one of several variables. I wouldn't worry about that either.
Skip the water. Foil the empty pan leaving airspace between pan and foil (this prevents scorched drippings).
The cook is still indirect but, yes, I guess one could say 'more of a direct cook'.
With a bit of an eye to timing I would say yes, you can get the briskets to finish at the same time --or nearly so-- especially if they are of similar thickness/size.
I foil by time, not by temp, and I foil roughly between the 2.25- to 2.5-hour mark. I'd get the briskets in, fat down, mark the time, then switch their positions about 1.75 hours into the cook. 45 min or so after that I'd foil each, then reverse their positions again. After 45 min in foil, I'd reverse again then cook another 30-40 min or so when I would check each for done.
At the temps I cook I do packers in slightly under 4 hours to maybe 10 min past 4 hours, hence my suggestions.