One major disadvantage of using the flash for timers/macros is you've killed a +$100 piece of hardware if you should wear out the flash.
The W25Q32FVSS Flash memory used on the Wemos mini quotes:
More than 100,000 erase/program cycles
More than 20-year data retention
It has 16384 256-byte pages (4MB). Finest granularity on erasing is a 4K block, or 16 pages. So that would be an issue modifying macros or timers. One solution is to copy the entire 4K block into RAM, make the change, and then write the 4K block back into flash.
The Wemos mini has its own 3.3V regulator from 5V, so a single 5V regulator can supply both the PIC and the mini.
Jeff