I wouldn't be so quick as to blame the rebuilder right away. The 2004R in stock form has more weaknesses than say a 700r4. The pump on mine grenaded, I know those are common, it's all over the internets. Put the right parts in a 200r4 and it's bound to run fine in a boosted car such as the GNs. My tired old 307 managed to kill a factory 200r4 so to say the rebuilders are the issue is almost irrelevant. A stock 200r4's weaknesses are more so the issue at hand here.
I agree with you on these transmissions being weak. I always heard the sun gear shell was very soft in the 2004r.
From past experience, having an AOD rebuilt for my Mercury Cougar, the rebuilder is usually open to suggestions of upgrades you may want done to the transmission to make it more durable. I researched common problems and solutions that are known to cure the weak spots in the transmission I was wanting rebuilt. For instance, I opted for a wider overdrive band that Ford start placing in later model overdrive transmissions (AODE/4RW70), stronger clutch materials, bigger servos and a wider shift ratio. I then sat down with the owner of the shop and we discussed what I wanted and he showed me the prices to upgrade and what was already included as upgrades to the 1988 AOD for my car, then ordered everything he did not have on hand.
Usually a good reputable transmission shop will have bulletins of some updates that have been recommended for the particular transmission they are rebuilding. Some may just flush the converter and rebuild it with a general rebuild kit for that transmission, fill it back up and call it rebuilt but others usually want the component to last at least the life of their warranty (if they issue one) and will make sure the TV cable is mounted properly and pressure is set before it leaves the shop. Mine even had me come back after 100 miles to make sure everything was breaking in properly and checked fluid.
Like I stated before and I am sure others will agree with me, HEAT is the #1 offender to any transmission, especially ones that sucked out of the gate to begin with! Throw a good aftermarket cooler inline with your radiator cooler, make sure to use the recommended transmission fluid, never flush a higher mileage or older transmission at one of those oil change lube shops instead drop the pan, change the filter and fluid every 30k miles or so and make sure the tv cable pressure is correct periodically to make it last.