The design of the '06 methodology is a two stage filtering. The mesh for the coarse particles and the bypass filter for those that could interfere with the particles that can interfere with the solenoids. Fine filtering is limited by the bypass function, and is further reduced during cooler transmission operation. For my truck which typically runs cool, I'm not in a position to determine if I just run operate in a low intensity situation or I have more fluid flow throw the cooler all the time. Never the less ......
The Job 2 design has a finer filter that should catch even the fines that can inhibit the solenoids and it filters all the time. How often do the solenoids have an issue, probably not often based on histories.
The modification does two things. It extends the fluid changes to 60k miles instead of 30k. So if your keeping the truck for another 120k miles it's a wash in costs. It provides better filtering. If you are one who uses Motorcraft oil and fuel filters, installs coolant filters and use both fuel and oil additives, this modification fits the mold. Again, 120k miles, no cost.
I had a hard time justifying this upgrade based on the mileage on my truck. Looking at the particles in the '03 version screen and Mark K saying the '03 in pan screen does not stop the fines full time that could interfere with the solenoids but the '08 filter would was reassuring to me I did the right thing. I'd rather improve my chances of not having a valve body issue away from home pulling my trailers.
But we all have to make our own decision on if modifications to our trucks are worth the cost and effort.
If you have a catastrophic failure in the trans, no filtering in the world is going make it any better. It's toast.