Yes, it's one of the things I would add. As you know, I'm not a huge fan of "Code". "System" is probably better (Mito is not fully committed to it in the new Laser!). Second 1u Alt is motivated by the Meta keys (diamond) in Icon mods. It's only one key and it wouldn't make sense to put it with the icons, therefore this is the most logical place. The Meta keys wouldn't necessarily be out of place with otherwise text+icon mods, imo.
Extension kits are not very popular. I have seen too many Alice boards without proper spacebars (when they were available in the extension kit). Hence putting only the necessary keys in there.
As someone who very much dislikes Code for a number of reasons (outlined
here and
here), I support changing all Code legends to System/Sys or Super. In that case, my proposition would be to add two 1.5u System or Super keys to the Extension kit, not Code. (By the way, 1u Sys in GMK Laser R2 was changed to Code for a different reason.)
As I said, I agree with the placement of the second 1u Alt in the base kit, if text 1.5u System/Super keys are added to the Extension kit to make it more purposeful. Otherwise, the second 1u Alt is useful if and only if the Icon Mods kit is purchased. It shouldn't make a big difference anyway since it's just one key, but I'm sure text 1.5u OS keys would be appreciated by a number of users (mostly Mac users, but also those who prefer OG HHKB key positions).
Regarding “necessary” keys, 1.5u OS keys are definitely more popular than the second 2.25u Shift currently present in the Extension kit, which is only used on 660 keyboards (of which there aren't that many, whereas any keyboard with a Tsangan/HHKB bottom row can use 1.5u OS keys). If you only count Western audiences, they are more popular than 2u Shift, 1u Shift, 1u Delete as well.
They should come in pair. It is in fact for ortho, as is the 3u and extra 2u. It's cheap.
Well, I think there is no point in including the second 1u for ortho in the Extension kit because
two of them are already present in the Ortho & 40's kit. If you have ever seen an ortho keyboard with four convex 1u space keys, please link it so I can take note
Otherwise, the second one can be removed from the Extension kit.
Besides that, 1u, 2u and 3u space keys are also used on regular ≥60% boards (most Alice-style boards, some ≥60% splits, Minila), so they serve a purpose outside of being just additional ortho compatibility.
Some boards have used two 1.75u spacebars (JD45). I see it more as an accent for Vortex Core.
JD45 falls under the same category as the JD40 that I mentioned (which also uses 2× 1.75u). If you want to count it separately, that still makes it only four keyboards in total that use a 1.75u spacebar, none of which are very popular, not even Vortex Core. It's fine if you want to keep it, but consider whether it's objectively common enough to warrant that (and also keep in mind that one 1.75u is already present in the Ortho & 40's kit).
Since there are no 1.5u spacebars (Atreus, etc.), these can serve as replacements. Also Minila has two convex 1.25u.
Again, two 1.25u space keys are already included in the Extension kit, which you have to buy in order to get Minila support anyway
No need to duplicate them in the Spacebars kit (that was the point of my comment). Also, Atreus uses two 1.25u/1.5u spacebars, not four, so the Extension kit on its own will be enough for that as well.
They're already included in the ortho set. Is there any non-ortho-40's board that could make use of them (convex 1u)?
Yes, convex 1u is useful for most Alice-style ergo boards (Alice, Lubrigante, Rukia, Maja, Type K...), ≥60% split boards (VE.A, Doppelgänger, Uni660...), etc.