You really can easily do all that with any Harmony remote.
I currently have four of them in my home (659/880/890/1000).
You will find Harmony to have discreet codes for many devices even the manufacturers say do not have them, so this often isn't an issue, but even so, it is an easy work around with macros (which the Harmony's set up with your guidance). I wouldn't worry about this with the Harmony's in the least, and personally think it's a pretty easy work around even without discreets, especially when you can get to a known state (on or off).
As for using other remotes, not a problem, if the Harmony doesn't get it right because it has to use a toggle rather than a discreet and the other remote changed it from what the Harmony remembers (this is the whole concept of Harmony's 'Smart State' technology), you just would need to hit the 'help' button which will walk the wife through fixing the problem, or you can easily add a power button to the display if you'd rather just fix it directly. FWIW my 890 runs my main rig which is a Meridian 861v4, and eight different sources, two HDMI switcher, TV etc and the wife can effectively use this system with simplicity.
I looked at the One, but it is pretty expensive and doesn't do RF, the 890 allows, and even included and RF receiver/IR emmitter for working components from long distances without line of site (you could easily use the same remote at the pool or in the office and control everything from afar.
FWIW Amazon seems to be the cheapest place to buy the Harmony remotes. The software is simple to use and very fast to swap around. Once you try a Harmony, you'll be glad to go rid of the MX-500 (I personally dislike them, they are sooooo cumbersome to program and without the smart state tech require very careful programming)
Check out the review I did of the 1000 for a description of the set up and programming, it's really easy to do. When I swap out gear in any of the systems controlled by one of these remotes, it genberallly takes me only a few minutes to switch it out, this even goes for pre/pro's and receivers, sources can be done in seconds. It usually takes more time for the program to re-load the data (especially in my 890, that thing has like 12 activities and every control for every component in the system) than it does to modify the programming.