You're right — I missed the bottom SPI-flash pads.
From the document available in this project, the key explicit note is that the ESP-12F has SPI flash pads brought out on the bottom row, and they are not usable as GPIO; they are only there so you can program the flash chip . For Flux pin classification, pins like SPI_MOSI/MISO/SCK/CS belong in Communication, not GPIO .
MISO, MOSI, SCLK, CS and any other bottom flash-programming pads
No Connect
only pins explicitly marked NC/DNC in the real pin table
My recommendation
For this part, I’d use these symbol sections:
Power
Control
Analog
GPIO
Communication
Ground
And if you want the symbol to stay cleaner, put the bottom flash-only pads into a dedicated:
Flash
That matches both the Flux section rules and the extracted note that those pads are not normal GPIOs
Important caveat
The PDF I could extract from your project does not include a full explicit pin table, so I can confirm the existence and special handling of the bottom flash pads, but not safely reconstruct every one of their exact labels from that file alone. The sync workflow explicitly says not to guess pin assignments and to use the datasheet as the single source of truth
If you want, I can do the next step and give you an exact per-pin Section assignment for every terminal currently in the part project, including which ones should move into Communication/Flash.