First of all, both are 1mm X 1mm. Newbie (aka Jarhead) said the following on his webpage:
"Some folks have claimed the Rebel die is smaller than the Luxeon and also smaller than the CREE die. It is not. It measures 1.00mm with a set of Multitoyo calipers, which is the same size as the rest of the recent die on the market."
Ha ha - I think he meant "Mitutoyo". Maybe there is an inside joke there. Here is the link to this site, which has a large quantity of big pictures (dial-up users beware):
http://www.molalla.net/~leeper/rebel.htm
The new K2 uses the same TFFC die as the Rebel. As for the Cree, they may appear to be bigger because of the small glass lens that magnifies the image of the die.
With the Cree XR-E, you can remove the dome and the metal ring if careful. Exposing the die to air will not kill the emitter. I have run the Rebel emitter and a Cree emitter without their protective lenses before. The Rebel die was in direct exposure to the air, while the Cree had a little bit of soft silicone around the die. Both worked fine! Actually, I have a Maglite Solitaire modified to use a Rebel 0100, and about 2 weeks ago, I accidentally pulled off the tiny soft dome by using scotch tape to hold the heatsink pill I made in place. It works the same as with the dome on. It is easier to scrape off the phosphors without a dome (causing the emitter to produce little royal blue artifacts in the beam), and it is also easier to burn yourself or other things. The LED die is extremely vulnerable to dirt, dust, sharp objects, etc without its protective dome, but it may be fine if totally enclosed and/or waterproof.
As for removing domes, you will notice a tint shift to a warmer white. This happened to me with removing the domes from both the XR-E and the Rebel. Also, after removing the dome dome the XR-E, you will notice a decrease in output. This is because all the light leaves the emitter at 180 degrees now, versus the original ~70 degrees.
If you could precisely position your emitter so the die is very close, but not in direct contact (remember the soft phosphors, and in the XR-E, the super fragile bond wires) with you special optic or device, then everything should be okay. Make sure everything is solid so vibrations do not cause then die and the object to get any closer. Could you explain a bit on what you planned on doing? The ideas seams interesting (if it is a special optic), and we could always help you further as needed.
Well, I hope I was of some use. If I was off on anything I said, please feel free to correct me. I forgot the half-width of a Cree XR-E, but I thought it was close to 70 degrees.
-Tony