Base Kit updated for the first time! A bunch of things were changed, take a look! The IC form has also been reset for new comments, so please leave one if you want to say or suggest something: https://forms.gle/ZMM2PhAaEbFcDkH28
Removing the squared Esc icon in favor of a white accent ⎋ is a welcome change.
Nevertheless, please consider some of the follow suggestions:
- Re-add the second R4 1u ⎇ — These are needed to populate a true HHKB/Tsangan bottom row.
 - Re-center the R3 ⌃ — IMHO this looks very odd raised.
 - Re-add the R4 1u ≡ and remove the ♦ — ≡ is usually used as an icon for Fn/Menu, this would make it coherent with the other 1.25 ≡ you used.
 - Consider using R4 1.5u ♢⌘ instead of ♢ — IMHO this makes the 1.5u keys look less "empty"; molds for these were made for GMK Burgundy.
 
Thanks for the suggestions! The R3 ^ is actually supposed to be centered, I'll fix that. I'll take the other suggestions into account as well, but I won't be doing the last one because it doesn't fit well in the set.
The updated base kit looks really good, so GJ Pachriksu for listening to feedback.
I agree with suggestions #1–3 from the quoted post (and highly disagree with #4). However, as far as #3 goes, I would keep both 
≡ and ♦ in the kit since having a generic R4 1u key is useful for a variety layouts (60%, 65%, 40% ortho — which, by the way, is currently supported). If there is one key that I would consider removing, it's the 1u 
⇧, since it's only really useful for 60% w/ arrows (GK64) and 40% ortho. But it's okay if that stays as well, although I wouldn't prioritize it (e.g. the second 
⎇ is a lot more important than 1u 
⇧).
As far as the 
♦ goes, one thing I 
would consider doing is replacing it with a 
>_ icon (examples: 
1 2 3). I think this icon would fit in better with the remaining icons, seeing as all of them are outlined and 
♦ is the only one that's filled.
If you want, you can use 
÷, 
× instead of 
/, 
* on the numpad; some people prefer those legends for aesthetics. I think that they would work well with this numpad because they're a bit more visually balanced than 
/, 
*.
One final thing to consider is including the following keys for minimal staggered 40% support:
- R2 1.75u ⭠
 - R3 1.25u ⭾
 - R3 1.5u ⮠
 
This would allow the base kit to cover the majority of popular 40s boards out there (standard 12u, standard 13u, Van derivatives etc.), which is why the 40% community has recently started recommending including these 3 keys in base as a good alternative for sets that don't want to run a dedicated 40% kit.
Together with the already existing ortho support, adding these keys would indeed mean that the set would have physical support for all of the most popular 40% boards overall.
Edit: correction