Just a heads up on something I found while messing with SPIFFS, the most up to date version of Arduino IDE still has the SPIFFS type definition .CSV files that reference EEPROM being stored inside spiffs and not NVM as it has been changed to, you can get the newly defined .CSV files from the espressif GIT repository here https://github.com/espressif/arduino-esp32/tree/master/tools/partitions one thing of particular note is that the old (1.8.9) min_spiffs.csv only has 61Kb of spiffs and the new one without the EEPROM definitions has the correct 190Kb.
arduino-esp32 1.0.2 and prior still used a partition for EEPROM emulation. Starting with 1.0.3 though it will be stored in NVS and the examples have all been updated. The “master” tree on github which you refer to is 1.0.3.
Once 1.0.3 has been officially released (currently only 1.0.3-rc1 is available) PIO will likely update to it. Until then there is should be no issues with compatibility unless you are mixing and matching versions.