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Bootloading a program via the optical programmer normally consists of a preamble followed by a hard reset, another preamble, program data encoded as 4B5B, and finally several '1' bits. Each mode (e.g. hard reset or optical calibration) is initiated via a sequence of 4 magic numbers. Optical calibration is done by repeating a series of calibration packets every 100ms, where the delay is manually tuned and set in the Teensy software (https://github.com/PisterLab/scum-test-code/blob/master/scm_v3c/teensy_uC_programmer/teensy_uC_programmer.ino#L1486). A detailed analysis of bootloading can be found in 20191014_Jove.pptx.
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