Yep, they changed up the rear of the case from the old 4-bolt ext housing to the 6-bolt and moved the rear x-member-to-trans mount from the case to the ext housing (though some of the pass cars w/one piece cases had the rear x member mount on the ext housing, as you know).I have a 6L90E from a Duramax with only 24K miles on it. Will be doing the same with my L31 based 383. I will be going to a 58x setup, DBW, and an E67 PCM with a modified late model Express engine harness to run it all. Just have not had time to dive off into it all yet.
Another thing that is rarely mentioned is the 4L60E transmission mounting point changed when the 4L60E became a 2 piece bellhousing even in the SBC era. Years ago when I put the 4L65E built for the older 350 as you previously mentioned into my 97 Express van I had to scrounge up a junkyard 1998-2002 1500 van aka 6 lug 2500 van crossmember to get the newer style case mounted into place. The mounting point moved and the crossmember on the vans bolt to brackets welded to the frame. 96-97 thus had a different crossmember than 98-02. I had to fabricate my own modified crossmember for the 4L85E swap later. My buddy also put a 99 Tahoe transmission in his 97 extended cab years ago, had to move the crossmember back and drill new holes in his frame.
As to why it's not often discussed, my guess is a combination of the relative ease of adapting cross members coupled w/the growing number of aftermarket companies that have purpose-built cross members for different vehicle-transmission combos and their respective mounting locations. Not surprising, given how popular engine and transmission resto-swaps have become these past twenty years or so..