The Allo Boss 2 did measure at least 20 dB better than the WXA-50 on the ASR bench in pre out SINAD. The WXC-50 should measure about the same.
Assuming both has the features you need, then I think it is an easy decision if you think you can hear the difference between 90 dB SINAD and 110 dB SINAD. Even under the worst case scenario, I doubt the WXC-50 would have SINAD below 70 dB and that's 0.03% THD+N!!
If you end up with the WXC-50, you can still bypass
The Yamaha's analog input will get double conversion, as the signal flow would be from analog to ADC to DAC so if you use it to control the volume you will lose probably another 10 dB SINAD depending on how good its ADC is, but again, can you hear the difference?
Considering the price it would seem the Yamaha is a better deal because in the US and Canada the price difference between the two is much bigger.
Based on specs and measurements, it is clear objectively speaking the Allo Boss 2 has better SQ, but subjectively I don't believe there will be audible difference, all else being equal, because the Yamaha's measurements were very good, much better than the only AVR measured, the RX-A1080, and better than any of the Marantz AVRs and AVPs measured (except the flagship AV8805 that measured marginally better).
Regarding your concern of double conversion if you end up with the WXC-50, you can use the analog aux output to feed the PM6007 and bypass the WXC-50's ADC/DAC.