I agree, all the Harmony options are very confusing. Add in all the discontinued products you see on Amazon, and it gets really confusing. I have 2 harmony setups. Both are controlled by Alexa, but I still like a remote. I find it easier to just select the channel or volume with a remote instead of calling out to Alexa, and sometimes Alexa won't hear me if the TV volume is too loud at the time I call to Alexa. Alexa basically turns everything on and will turn to the device I request. Then I generally switch to the remote to navigate the menus in the apps, etc. I have a dot specifically for each harmony setup.
My main setup is the Harmony Elite, with the home hub and touchscreen remote. Fantastic product, but it is a bit expensive. Took a while to set it up, but I customized it with one-touch commands to watch Netflix, Hulu, HBO, Prime Video, etc. and I even added icons for each command, and even customized the touchscreen menu for each device, so it is very intuitive. My wife doesn't yell at me about "all the stupid remotes". This is the best option if you have several pieces of equipment -- mine controls TV, Apple TV gen 4, Fire Stick (which is being moved since Prime Video is now on Apple TV), Blu-ray, WDTV Live Hub, soundbar, and stereo receiver. Dot is connected to the receiver, and receiver has speakers in 3 rooms, so I can use it to play music throughout my first floor just using voice commands.
My other setup is a home hub (which came with a free Dot when I ordered) with the Harmony Smart Remote addon. This is just a TV, Apple TV gen 3, and blu-ray, so the 3 device buttons on the remote are perfect (I know you can control 6 with this remote, but don't like double function buttons (long-press, short-press)). I did use black label maker tape to label each input for my wife. Again, Alexa turns everything on, but then we generally switch to the remote for navigation and volume. This setup is in our home gym, so it is nice to have Alexa pause and play a video or change the channel.
It did take me a bit of trial and error to get the Apple TV macros to work to open specific apps, and there are subtle differences in how the gen 3 and gen 4 Apple TVs respond to the harmony commands, so each setup is a bit different. I did find the desktop software a bit easier to program the devices than the iOS apps, and I felt there were more options for editing on my PC than in the apps.
Because I have 2 Harmony hubs, I do need to use a second Amazon account for the second setup, so I can't enable voice recognition for our echos, but that's not an issue for us.
Either setup is highly recommended, it just depends on what you want to control and how much you want to customize things.