I really don't believe supercid is the issue. Most all modded phones have supercid and have been flashing ruu and ota fine since the beginning. Every second thread would be about ruu or ota bricking their phone, but instead it is only a small handful of users.
We have most users complaining that their modded phone, that likely had supercid, installed the JB update fine and now have the "touch screen wont work on CM10" issue.
I think you need to consider it is something else that is bricking phones as literally millions of ruu and ota have been installed fine with supercid. Ruu and ota flashing is the major reason for supercid.
Perhaps it is just AT&T phones in particular that had the cid changed to get unauthorised unlock tokens that have the issue. Maybe the phone is failing some other check and getting stuck in limbo?
The SuperCID problem really only applies to people flashed to different carriers or ppl trying to ruu. The details of why are not fully clear, but there have been enough ppl between Evita and Jewel (especially on Jewel because to s-off an ruu needs to be run)
Part of the problem is because the ruu checks various version info stored on the phone (such as cid, and various NV items) which has different information than the actual firmware installed. This causes the ruu to flash some firmware files and not others. When it comes to certain firmware, you must have compatible versions.
Unfortunately what I described is just an overview. A fix requires knowing the exact details and manipulating additional files/partitions. But, while we know "generally" what the problem is, we don't have all the details needed to fix it. Couple that with the fact that there is no way to recover from many of these bricks, making testing very difficult or impossible.
Jet (and the process it automates) is largely a hack. As such it comes with a higher than usual chance of problems. As we see, some of these problems are more of a side effect, not showing up until some time later.
Hope this helped clear up some things. Although even we the developers don't have all the answers.
-SLS-