I don't think that we can issue a blanket statement and say the auto is useless.
The problem with the 3L/ATX before was mainly from the modified high-stall torque converter and not the other tranny mods.

It seems to me that the answer is to take a healthy CD4E and mating it to a 3L with proper planning in mind. Use the stock converter until we find out through multiple swaps if they are strong enough or not. The converter may not be the weak point, it may just be clutch pack strength. Everything on the transmission may work fine.

The areas where I could forsee issues with the 3L/ATX literally would be how much clutch area is in each clutch pack. More torque may mean it will slip more than designed with each shift and wear out quicker. It may not though.
Why can't someone start searching around for better clutches? Is ther room in the clutch packs to increase the number of clutches and steels by one or two more?
Combine stronger clutches with the faster shifting valve body (like the sonnex ones?) and maybe you will have a transmission that will handle a 3L for the long haul.
However with all that said, just pick up a couple of used ones from the junk yard as a backup for the stock one. Run the stock one with a 3L and see how long it lasts.
Plan for the future that now you will use the atx and see how long it lasts in stock form with the intent to build a stronger performance version that you can put in later.

Former owner of '99 CSVT - Silver #222/2760 356/334 wHP/TQ at 10psi on pump gas! See My Mods '05 Volvo S40 Turbo 5 AWD with 6spd, Passion Red '06 Mazda5 Touring, 5spd,MTX, Black