I believe the issue was first found by one of the installers, max psi was less than required to turn off the TPMS (44psi max if I remember right).Just looked up your tire; load of 2149 vs 3000 or so for E-rated. My XL rated is 2756, or 10% less than an E, 34.8 lbs. vs like 51, 51psi max vs 80. Well, only you know if you need the capacity, and if so, ride quality should be a lower priority.
I had ran into this exact same issue without realizing it on a dodge 2500 where NTB was tasked with installing tires on wheels I provided, then installed the package on the truck. In that case a D tire was installed (all that was necessary since my dad got his own 2500 to haul his camper, wasn't a heavy truck to begin with and truck did not haul heavy loads after that so D would have been fine at this time) and some management person called me personally a week later to ask that I go back and have the tires swapped for the E version of the next best tire available in that size (a BFG KO2) free of charge. I naturally obliged.
Then after riding on what felt like wagon wheels for a week, I lowered my pressures to 60/40 and used the light load setting to keep TPMS off. Over time I ended up running much lower pressures and dealing with the light just to get a tolerable ride. People in the cummins forums have spent hours discussing and researching tire pressures with pretty similar suggestions across the board.
That said, my capacity is a minimal camper style setup/mtb hauler. No towing. I had not really researched the differences in load ratings that deep, only having read a few things on here. My dad, who was with me, believed they only intended on replacing the rear 2 tires. It's a T250 transit FYI.
My understanding is I have came upon the same predicament now in my transit, a tire was installed that does not meet what their computer deems "safe" aka "liability". They are eating the extra cost here as well.
To answer your question, yes ride quality is the priority over hauling. Is this XL load rating tire available in the cooper RTX, if not is it available on any AT tire 245/70-16? The information on this forum as a whole is great, just takes a lot of digging to get a culmination of solid facts.