@Will-Dickson Thank you so much for the suggestions. I could make it work with the AVRISPMKII programmer. Also, your modified firmware, especially the makefile was very helpful and made my work absolutely easy. Thank you once again.
Yes, the XL transilluminator does fit inside the imaging enclosure. It is a snug fit, but it works. Unlike the Small, Midi and Large transilluminator, you do have to take the door off in order to take the transilluminator in/out of the enclosure. But if you are planning on keeping it in there most of the time this shouldn't be an issue I would think.
There is an adapter we ship with the XL version, which is not a frame but a base plate for the transilluminator to sit on.
I have added the Extra Large XL option to the product page now, so you should be able to select it.