I sort of tend to agree with blendo75, but with some big caveats. I end up rehashing my feelings on the unreleased stuff occasionally, I guess it's time again now that things seem to be heating up again.
I feel that Play By Numbers is the only one to have had an actual local limited release. It's the only one that was pressed to CD on its supposed initial release, there's a couple anecdotes of people having recognized the artwork from the local record stores, and according to interviews, it was the first time they used the name Boards of Canada (I think they said 1994, not this specific release, so its reading between the lines) at that point, they were probably just now making a go at being a shoegaze band, the stuff they'd doodled around with and put on Catalog 3/Acid Memories/Closes Vol 1 was totally different.
Hooper Bay seems like it was probably a dry run for Twoism, it was supposedly pressed to vinyl as well. Maybe they didn't like how it turned out. Maybe they didn't have confidence in their sound yet - its a total 180 from what they were just doing and I'm sure it was back to just the Sandisons at this point, maybe Chris Horne too. The decision to change it up so much is really interesting to me. Did they eat some acid, start listening to SAW2 and decide to watch that tape of Sesame Street that turned into such a goldmine of samples? Anyways, vinyl seems like the largest commitment, format-wise so it seems weird to press it to vinyl and then do nothing with it. Maybe a few copies did go out to local shops, who knows. Twoism was distributed on vinyl to members of a mailing list and that's how it became known, so its weird that they committed to vinyl for Hooper Bay but made no attempt to distribute it.
Maxima and Old Tunes were sent out as demos to record labels and given to friends and family as well. The reason they leaked was because it wasn't just friends and family in this case. The former was a more developed picture of their modern work, Old Tunes is likely the less developed sketches that were a mix of things made prior and after Play By Numbers that didn't get onto any of those supposed "proper" releases. It's hard to tell what was made when, since PBN is really just an aberration in their catalog. They went back to making the same type of music, albeit better written and with more of their trademark flourishes now in place, so I feel they just mixed together the stuff that was contemporary but didn't make the cut for Maxima along with some of their other old music.
My theory on R35TT is still that its a compilation of the best and most consistent work from those "proper" unreleased tapes. It's Goldilocks, it's just right. Old Tunes veers erratically from juvenile ephemera to mind blowing stuff like Boqurant/5.9.78, Kiteracer 2 and I Will Get it Tattooed but R35TT is just all killer no filler. It's somehow more developed than most of the OT but also more primitive at the same time. Very hard to explain for me but its fantastic.
With regard to Catalog 3/Acid Memories/Closes Vol. 1 and the associated artwork "controversy", I think it's really simple. These things were just simple handmade cassettes along the lines of the OT prior to 1997. Their website in 1998 only listed Acid Memories, Play By Numbers and Hooper Bay. No reference to any CD releases other than Play By Numbers. However, Acid Memories did have its CD shaped artwork and "Boards of Canada" titling (whose name did not exist when it was supposedly created) at that time so its safe to assume that Acid Memories was put to CD at the same time as the others, it just didn't say anything about it in the entry. Maybe a year later, Catalog 3 and Closes Vol 1 were added to the website, along with a note about their CD reissue in 1997. Basically, my thought is that in 1997, they pressed (burned?) all 3 of them to CD, gave them proper covers, had a Red Moon party to celebrate signing to Warp and handed them out to friends, never to be sold in a store. The end.