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If not, is there a recommended way to build MicroPython from source with OTA support specifically for the ESP32-S3?

Yes, define your own board. See the README.md in https://github.com/micropython/micropython/tree/master/ports/esp32 .

You can copy the relevant files from another board.

In my build tree, I have the following structure for my boards subdirectory:

├── ESP32_S3_N16R8
│   ├── board.json
│   ├── board.md
│   ├── mpconfigboard.cmake
│   ├── mpconfigboard.h
│   ├── mpconfigvariant_SPIRAM_OCT.cmake
│   ├── partitions-16MiB-ota.csv
│   └── sdkconfig.board
├── ESP32_S3_N8R8
│   ├── board.json
│   ├── board.md
│   ├── mpconfigboard.cmake
│   ├── mpconfigboard.h
│   ├── mpconfigvaria…

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Answer selected by jonnor
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