Car Code does command TDCO and appears to have the capability to do timeset. There is no KOKO relearn necessary with it. I cannot speak for AE as I have never used it. Does this answer your question, Buddy?
It is a noticeable difference in power and mileage. It is worth the effort in my opinion. Just the sound at a cold idle makes it worth it to me. I get a lot of compliments when she is just sitting there idling.
The setting is stored in the PCM, so yes, you will have to do the TDCO again. But now that you have done it, you know it's possible and you even know the tricks now.
You definitely need to set the timing to take advantage of the tune. Check out this thread:
http://www.thetruckstop.us/forum/showthread.php?t=9198
This is something you definitely can't do by ear.
Lance, what is your timing set at? I am running Bills' old tune, Max-E-Tork, and am still impressed with the power. When I put it in, the difference was night and day. As a case in point, with the stock tune and my 18' trailer loaded down with the wife's car, I struggled to top Fancy Gap pass...