No there not currently any polarization control elements in the engine
No there are no isolators in the engine.
A k-clock interferometer and associated electronics/filtering generate a pulse train that is linear in k-space. This is explained in further details in this paper.
You can use the trigger output as a sample clock generator for your scanner’s arbitrary waveform generator so that the scanners are synced directly to the A-line trigger. Refer to the electrical connections to find the SMA trigger output connector on the benchtop and the small form factor OEM, as well as on the Integrated Engine next to the ethernet port. For the standard OEM engine, the SMA trigger output is provided using the interface board.
The power plots in the test report are a single sweep power as a function of time. The OSA trace is integrated power over a long time as a function of wavelength. The shapes described are normal; the laser tuning slows down at the edges of the sweep (spends more time there) so the OSA integrates longer there artificially distorting the spectral shape to give the "batman" ears on the edges of the spectrum.