I have one of the 4806 which was upgraded by DENON into a 4806CI ( at a cost of $700+).. I have the original remote and indeed it provides access to features you would never think are necessary.
The DENON techs are the best....if there is a firmware update, they will tell you where it can be found.
Though, I have a Logitech Harmony One as well.
With patience and a few calls to Logitech, you will be able to add most if not all of the adjustment features found on the DENON. Better yet, place them in a sequence that makes it easy to find and use them to control your unit.
The issue as I see it, is Economics.....buy the EBAY unit and never be sure it was'nt dropped, items spilled on it etc. One benefit, the batteries see to last forever. The Harmony is still among Logitechs best and costs about $150 .00 new....on EBAY. and can be used on other units and products.
The 4806 is a monster power house and musically among the best sounding unit for the time..... I only wish it had two LFE outputs.... using a splitter drops the output signal somewhat.
Good luck with your efforts!