True, but there are many AVR controls that are either not available, or quite cumbersome on the Harmony... at least on mine. The Harmony is convenient for pedestrian every-day use, but I still keep my AVR remote handy, and use it quite a bit. Also, the Harmony is not particularly ergonomic in my opinion. If my AVR remote died, I would quickly replace it.
To the OP, sorry, but I've never had to replace one and don't know where I would start. I suppose a call to the mfg would be first.
All the AVR controls are available on the Harmony if you hit "Devices" then "Receiver" or whatever you named the button. This is helpful, for example, when you have the remote's primary Menu, OK, and arrow keys set in an activity to operate your HTPC, Roku, Oppo, or whatever; but you occasionally want to activate and navigate the AVR's Menu. For quicker access to more commonly used buttons (like the Movie, Music, Game, and Direct buttons), just set them in the "Additional buttons" part of the activity to make them available as soft keys. As I mentioned before, a little patience helps when setting the remote up.
The only functions the Harmony can't perform are the press-and-hold functions on the surround mode buttons. I prefer the "Auto" mode on my AVR, almost never using the virtual surround modes; so I haven't missed the press-and-hold thing. If I ever did want to switch from Dolby PLII to DTS Neo:X or some other such nonsense, I'd probably just use the Android app.
Re: ergonomics, there are a few different form factors -- some of which have been discontinued, but are still easily found on eBay. The Harmony One (what I use) feels comfortable to me, is large enough not to get lost in the cushions, and I can operate the playback controls, menu / guide / etc, and arrows without ever looking at it. The Harmony Ultimate might be a better fit if the user almost never uses the number pad and prefers something a little smaller. The Harmony 1000 or 1100 would be good if the user wants to look like a Bond villain. It's all a matter of personal preference I guess. It's not like the stock Marantz remotes offer any sort of spa experience in decadent luxury, anyway.
The best part about about Harmony remotes is also the worst part: one remote manages every device in your chain. If you are accustomed to having his-and-her remotes in the room, you're not going to have an easy time. If your wife powers on your TV using the cable box remote, for example, your Harmony has no way of knowing the cable box and TV have already been powered on, and therefore will not work as intended. If you do get a Harmony, be sure to remove the batteries from the rest of your remotes and put them all in a drawer or closet.
