Very cool idea! I think the HHKB layout lends itself quite well to a mobile keyboard, which is what I'd use a Bluetooth keyboard as. When saying USB Type-C, does that mean it can be charged via USB or can it also connect to my PC via USB without using Bluetooth?
You're saying the controller won't be pre-soldered onto the PCB. What kind of package will it come in? If it's not easy to solder for everybody you might want to consider changing your angle on that.
On the split spacebar sizes, I want to say that 3.5u keys and even 3u are a very bad idea. Even if you manage to get them made, it will be neigh on impossible to get custom keysets for this board and I can imagine most people would use one of the alternative styles because of that. Stick to the standard keysizes for the lower row, 2.75u, 2.25u, 1.75u, 1.5u, 1.25u, 1u. Everything else will just be a major hassle. On that note I'd recommend to incorporate as many spacebar layouts as you can without overlapping the pads too much. If they do overlap a lot, the holtite sockets will fall out easily, which is not what you want at all. Take a look at the YAS62 for inspiration, it had a lot of good ideas in that regard.
Wireless charging seems a little useless but might be very cool if the keyboard has a bit of space underneath so I can actually type while it's charging.
Either way, I'll be following this!