Chinook and some known pre-Twoism songs were played at early, unrecorded live shows
There have been rumors of a short snippet of a live Chinook performance being hosted at one point on the old EHX website, though nobody seems to have saved it. At one point I navigated to a directory structure in the Wayback machine that had all the old RM samples, but lost the link. There have been some (unconfirmed) eyewitness accounts that they played all of Play By Numbers at a 1997 performance (which may further suggest the use of their voices on that album or possibly just on stage otherwise how would he/she know that?) and if that's true who knows what else they played?
Chris Cunningham has some of the Geogaddi outtakes and/or live ATP tracks
BoC claimed in an interview that they gave Chris an hour and a half of new material, this was around the Geogaddi era, and the Telecom Italia song appears in the ATP set. Maybe he knows the titles and has the studio versions but isn't saying anything about them because he knows that M&M will break both of his legs if he does? Also, there's the case of whether ATP Track 7 is either Hooper Bay's "Noatak" or a Geogaddi outtake, which brings me to another extremely forced possibility:
Noatak was brought back for more polish to potentially be released on Geogaddi
But then it was later turned down in favor of the tracklisting that ended up being released. Yeah, I haven't really got much reasoning for this one besides that half-connection.
Acid Memories had Mike and Marcus' voices on it at some point
For some reason my brain drifts to Acid Memories when thinking about this theory, though it really could be possible for any of the 5 mystery albums. Could be one of the reasons why they're so apprehensive about releasing them. Think about it, how many times have they allowed for their voices to be recorded and released in the past? I can think of exactly one (the 1999 John Peel interview).
The original Catalog 3, Acid Memories, and Closes Vol. 1 artwork are completely different
It makes sense for Play By Numbers and Hooper Bay to have square, color album artwork since the former was released on CD and the latter on Vinyl, but the first three have all kinds of holes. Catalog 3 and Acid Memories both use the full "Boards of Canada" even though that didn't happen until 1994, Closes Vol. 1 has "97" blurred out of all the spots where it was present in the original PIC photo project, and almost all of their discovered old tapes so far have been black and white photocopies. It's possible they made new artwork for the limited '97 CD reissues or in Acid Memories' case specifically for the purposes of matching the format of the website at the time.
Tomorrow's Harvest has more unreleased material than any of their other albums
MDG has stated that the brothers are never not in the studio and that they're very prolific behind the scenes, and if that lead to 90+ unreleased tracks in the Geogaddi era then how many could have been made for an album with a gestation period that was about twice as long?
Acid Memories tracks were later reformed into Campfire Headphase tracks
People have noted similarities between ATP-09 and a couple of Old Tunes to Tomorrow's Harvest tracks, and if TCH was a sort of return to the "guitars meet electronics" sound that Richard Southern described AM as having then I think you can see where this is going.
Play By Numbers contained vignettes in the style of Twoism
I was pondering "Wouldn't You Like To Be Free?" and trying to think of directions that the track could go in. At 5:40, that's kind of a lot of time to fill. I couldn't really see the track running longer for maybe 4 and a half minutes, but then something clicked. Play By Numbers was their shot at imitating MBV and MBV practically invented musical vignettes, who else thinks there might be slightly more than 5 tracks on that CD? Topping that, maybe these vignettes consisted of little electronic ditties that may explain the "Shifting further into electronics in other [places]" in Richard Southern's description. Maybe that's what some of the shorter R35TT tracks are. (A04, B08, and B10 come to mind)