I don't think you would find programming via wireless small. That part of the requirement would be difficult.
Indeed I’m thinking about droping that requirement for the first iteration of the device…
The main processor part you can reduce in size, but when you do, the FTDI programming header will not be a direct fit and you would have to solder the wires.
Soldering is no problem. There will be lots of soldering anyhow.
I thought for the main processor this looks interesting:
Although it could be smaller, and out of the box it is not wireless, it may do the trick for the first iteration. Thanks for the link!
Sound like the Moteino might be the MCU your looking for.
For my use case, I don’t see an advantage over the TinyLily. Both are not programmable wirelessly without an additional adapter, and the TinyLily is smaller.
Can you do it with an esp8266 ESP12 or ESP14 module? Peripheral selection shits but they're dirt cheap, popular (so lots of info) and fairly small for a full module with most of what it needs to work...
Can you program an Arduino over the air using these modules? (doubt it)