Yeah, from what I’ve been told about it the 41F-1 was nothing more than a limited supply batch meant for testing purposes for aircraft prototypes that didn’t have the need to fully interface with multiple stages of EEC.
If there were to be any mishap with a prototype running the 41F-1 then it would need a computer on the airframe side that could properly interface with the EEC’s secondary control mode. That’s a bit of money and a bit of extra development time needed to slip that in there, so my best guess is that the T-50 lineage used the 41F-1 for its reliability in the case of emergency. There were only about 2 dozen or so that were ordered for PAK-FA development.
The 41F-1S being used on active serial airframes sort of necessitates extra digital failsafes, and there isn’t as much constricting a full-authority setup.