The next day after having transmission rebuilt the high coolant temperature came on

In and of itself, no. However, what was removed is the question. Did this happen as soon as the repair was done?

You mentioned there were no leaks under the vehicle. Is there any evidence of a leak? Honestly, I see no reason for them to have drained the coolant from the engine/radiator. The engine is supported without removal while the transmission is removed. The only thing I can say is maybe by accident they drained it. However, that would have been in error. The reservoir may have been moved for a reason, but the radiator and engine would have still been full and prevented an overheating issue.

When you refilled the system, how low was it? I realize the reservoir was empty, but did it take more than that to refill the system?

Please keep in mind, what I am saying doesn't mean they didn't accidentally damage a hose or cause one to leak, but you indicated there were no leaks.

Joe