So it seems we're all agreed that the Marvel titles which take place in the 616 Universe but are not otherwise part of the order will later be included in an Appendix Order of some kind.
The thing that has always felt off about this to me is that such an order would represent one of the most unreadable reading lists ever compiled. As unlikely as it is for me to ever finish it, I really
want to get through the whole CMRO. I can't say the same about an order which is comprised of eight million issues of Kid Colt, Rawhide Kid, and golden age Human Torch stories.
I've come up with what I feel is an elegant solution. Instead of keeping these issues fully segregated from the order in a separate list, include them sort of as footnotes to the order. Let me explain.
Say you're on issue 293 of the Order: Strange Tales #141 (February 1966). Somewhere on the page (e.g. in a separate tab, in an existing tab, in a table, etc) it says something like "Appendix Issues released February 1966: Rawhide Kid #50, Sgt Fury #27, Millie the Model #135, Modeling With Millie #45, Patsy and Hedy #104". Each issue would have a checkbox for users to mark them read.
These issues wouldn't be fully part of the order; no effort would be made to give them a number in the order or fit their arcs in to the mainstream order. Character appearances wouldn't be tracked or cross-referenced. It would simply be a way for users to track their reading progress with them if they want to. And I'm sure many will initially object to my inclusion of the romance books in the above example, but for a feature like this, there's really no reason not to be fully inclusive; it really doesn't hurt anybody who doesn't want to read them, and it just might help somebody who did (for whatever weird reason, I'm not judging

). It would even be cool for users to be able to specify on their account page what appendix titles they want listed, so if they only wanted to see Sgt Fury, they could just see that, or if they only wanted to see westerns, they could just see that, etc.
I like this system because it satisfies the completionist in me by having everything listed at least just for reference purposes, without making a whole separate order that I'm sure would pretty much never be used.
A pre-FF#1 order (or at least just a checklist) would still be required; this solution would only really work for those issues concurrent with mainstream Marvel, but with the westerns, Sgt Fury, Captain Savage, and Conan the Barbarian, that represents a large chunk of the non-mainstream issues (and especially if you include Millie the Model and Patsy Walker [these characters both held multiple concurrent titles and had runs of hundreds of issues, and yet are virtually forgotten these days ... I know that at least Patsy Walker's stories are retconned to be in-universe fiction, but that still makes them a kind of canon, and their characters are referenced in the mainstream canon a handful of times]).
Also I would still be in favor of a full, separate appendix order for the Ultimate universe and the 2099 universe, since they're not 616 and I'm pretty sure a lot of people would be really interested in reading them.