The tar packages are meant to be as close to stock as possible. I only integrated root into them because Samsung blocked the zergrush exploit.
If I integrated EL29+CWM into this package, then flashing it would give you a yellow triangle and increase your flash count. It isn't that much effort to do so, it just has that undesirable side-effect.
So basically the way I package these is you get stock everything, except a rooted ROM. This won't trigger a yellow triangle nor will it increase your ODIN flash count.
Then you just go to the Auto Root package and choose Option C to install CWM (also without triggering yellow triangle and not increasing flash count)
I usually integrate in chris41g's stock+CWM into the Auto Root package, but he hasn't released one for EL29 yet.
In the mean time, you could either
1) use EL26+CWM and when you are done with CWM, switch back to EL29 (assuming you want the EL29 kernel)
2) run EL26+CWM (or any kernel+CWM) with EL29 modem/ROM
3) use the generic zImage/BootImg install feature of the Auto Root package to install EL29+RogueCWM from
this thread. You basically extract the zImage from that zip file and place it in the copy2sd\000root directory (of the auto root package), then choose Option C and Install Generic BootImg.