I am considering a Tacoma. If I get one, I must get a cap. And I must be able to open the rear window of the cab to allow A/C and heat into the cab because some of what I transport must be climate controlled. Will a cap let me do that?

to a certain degree yes, i think it'd depend on the insulating qualities of the cap itself tho, bear in mind that you'd be heating/ cooling the cargo area with you're in/ under dash heater and A/C system, to get the cargo area heated or cooled may make the driver and passenger uncomfortable.
just my .02 worth!
Rick, Ore