This is what I'm wondering too.
The manual lists 90Hz as the "Cut off frequency", and doesn't go into any more detail about whether it's a high pass filter or not, or whether it's affected by Pure Direct or not. The screenshots above show that a "crossover frequency" is configurable via the mobile app, and suggest that is related to YPAO being enabled. It's not clear whether this crossover adjusts the "Cut off frequency" referenced in the manual or is something completely separate to that. These are separate to the bass, treble, balance, and loudness controls which are set via individual physical knobs on the front panel.
Then the manual only says the below about Pure Direct mode:
Enjoying pure high fidelity sound (Pure Direct)
When the PURE DIRECT switch is turned on, routes input signals from your audio sources so that the input signals bypass the BASS, TREBLE, BALANCE and LOUDNESS controls, thus eliminating any alterations to the audio signals and creating the purest possible sound. The PURE DIRECT indicator lights up and the front display turns off after a few seconds.
No mention of anything about "cutoff", "crossover", or even YPAO. I can understand YPAO not being available in Pure Direct due to all the DSP it uses but am not certain if that also includes "cutoff" or "crossover" functions. The Pure Direct modes on some of the Marantz amps don't appear to affect the subwoofer crossover settings, according to the manuals anyway.