Seems there is some confusion, this is not a CR250 ignition. A CR style stator backing plate that is the extent of parts sharing. The CR ignition was not optimal for the TRX application as you seem to have recently discovered. Gen 2 of this ignition was used on the Service Honda 2 stroke development quad in 2003! We are now on Gen 3.5 for anyone counting. Development continues on this system to this day, literally.
The universal CDI you mention, with the old stock permanent magnet fly wheel from the 80's and an adapted stator I am sure is wonderful for a guy that wants to make his own map spending a day on a dyno for specific combination, perfect, for turbo and drag race guys where low to mid speed running is not a major concern.
However for the vast majority of riders that ride recreationally trails, dunes, tt racing ect. the Service Honda ignition presented here may be a better choice for the following reasons;
1) Optimized low and mid speed running, where most people ride.
2) Optimized modulated response, where most riders spend the vast majority of their riding time, with no compromise in top end.
3) The ability to run electrical accessories, like lighting or a fan.
4) Easy setup install and go. No shipping parts around to be modified. You take your existing ignition off completely, install and ride. You then have a complete system that you can use as a spare or sell.
5) Stable development, with continued backward compatible upgrades.
6) Long term serviceable, components like the stator can be replaced easily and have several suppliers that can be used in a limited availability scenario or for use in more remote locations where a U.S. based parts supply will take time to arrive.