I got it back out and took photos. While I do feel those differences you mention, it still doesn't get it to fit. It is off in millimeters of space, sadly.
Oh my! I see!
I was looking through my inventory list for something else and it shows I have two Crypt boros. So I looked through my Vaperz Cloud stuff and sure enough, there are two of them. I grabbed one and grabbed a SXK Billet Box and it is snug. Not tight enough to get wedged in there. At first I thought it had to be perfectly level to fit. But playing with it I can put either the top or the bottom part half way in and tilt the other end in and it drops right in. Pretty much like the original boro does. Almost no play left and right. And quite a bit up and down. Picture shows it completely up.
Gosh... it is pretty dirty under magnification.

