Ok, I will be "That Guy"...I am by no means a transmission expert, so I'll lead with that.
When looking at it from strictly a financial aspect...my thoughts here are that despite the possible lower quality build that you'd get from a GM transmission...the fact that you would have a nationwide warranty that can be utilized at all GM dealerships that includes 100% parts AND labor, and it's even a little cheaper on the front end purchase...I would definitely go with the GM unit here. Additionally, a lot of GM dealerships offer complimentary loaners, which would be another added perk of going this route.
Lets think in terms of "what ifs".... What if the transmission you purchase (regardless of independent shop trans or dealership), fails once per year over the next 3 years. Which route would cost you more from that standpoint?
The GM route just (to me) seems like it would be the least "financially volatile" route in my opinion as everything I have been told by my local GM service manager is that the warranty that accompanies those transmissions is 100% no frills, no cost warranty with no deductibles.
Hope this helps!
Tell me more about the "nation wide warranty" while I book a room and try to get a rental car for my family road trip that got interrupted by the Genuine GM Product with a nation wide warranty. Oh, the local steelership in my random breakdown town can't get parts for a month or on the lift for two more months.
Have the local shop that builds transmissions daily and knows what aftermarket parts are good to go rebuild your transmission before it grenades the case.