Finally the power supply modules arrived, and I could finish the layout.
And sizes seems to be fine, and with enough clearance too.
My first plan was to just use serial between the ESP8266 and Atmega329P, but I changed that to I2C instead, with a pair of BSS138 for level shifting.
A bit more love to the silkscreen, and it looks like I am ready to order the first prototype. 😉