Couple of reasons.
First, the hub isn't battery powered. Since it's plugged-in, it can maintain persistent bluetooth and wifi connections which don't need to be reattached every time the user wants to use their remote. This persistence also allows Google Assistant and Alexa integrations. When I walk from my bedroom to the living room, I often call out "Hey Google turn on the TV". Silly, I know, but I like it. I also use Google Assistant to remotely turn on my air conditioner on hot days while I'm on my way home from work. This works in routines also, so when I leave the house my lights, fans, and A/C all turn off. Standard smarthome stuff.
Also I may be talking out my butt on this one, but since it isn't power constrained, it also seems to shoot out a vastly more powerful IR signal than any handheld remote I've used. Even inside a partially obstructed cabinet it has no problems turning my TV or A/C on via IR.
Second reason is the separate hub allows the handheld remote to use exclusively low-power RF signals, meaning it doesn't need to be aimed at the device you want to control, it works under a blanket, even in another room, and the remote's battery lasts *forever*. My simple little harmony smart control remote uses a button battery and it easily lasts two years of daily use. I have one in the bedroom too, use it a lot less, and I don't think I've ever replaced it over like 7 years.
The app is something I don't use particularly often, so I wouldn't be at all upset if it was a webapp or electron or whatever. It's fine if something I open every 6 months uses a gig of RAM. What matters to me are features, UI design, and ease of use.