Have you tried using the analogue of what is described in the Adafruit guide with PlatformIO tools? PlatformIO is well-capable of using the latest version of e.g. Arduino-ESP32 (docs) as well as changing board definitions to use a different variant folder etc.
So as a first try, you should create a new blank Espressif ESP32 Dev Module + Arduino project, then change the platformio.ini to
[env:esp32dev]
platform = espressif32
board = esp32dev
framework = arduino
platform_packages =
toolchain-xtensa32@~2.80400.0
framework-arduinoespressif32@https://github.com/espressif/arduino-esp32.git
board_build.mcu = esp32s2
board_build.variant = adafruit_magtag29_esp32s2
and e.g. a blink sketch.
See also related topic Update to the latest version v2.0.0 from GitHub.