I was going to leave this alone as it makes no difference for myself
however, from to the Yamaha CX A5100 manual and this applies to all sources.
"When Pure Direct mode is enabled, the unit plays back the selected source with the least circuitry in order to reduce electrical noise from other circuitry (such as the front display).". It does not indicate that all digital circuitry is bypassed for analogue sources in Pure direct mode, although a circuit diagram would be able to confirm this. However this Yamaha diagram from their site for the Z9 flagship AVR, circa 2004 seems to indicate that analogue inputs do not bypass the ADC section.
Perhaps I am still misunderstanding and the diagram is incomplete.
That said, what is the point in using a £2.5K surround processor, bypass all of the features and functions for, as suggested, minimal if any benefit which could literally be replaced by a £10 analogue switch for that "special occasion". This would not require the processor to be fully on (standby not being an option), cut the signal path down even further and remove any erroneous conjecture on my part.