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I use Sonos 5 + Sonos Sub in one room. Sonos Port + Yamaha receiver in the second room. Yamaha creates a small reference when processing the sound. Is it possible to generate a time reference to other Sonos devices (all other devices except the Sonos Port) while playing (a few tens of milliseconds).

No.  You need to find a mode (Direct, Pure, etc.) mode on the Yamaha that bypasses all DSP enabled modes.