Yes, it allows you to prevent your ISP manipulating your DNS. Your ISP has no way to know when you are resolving, because it is masked in other HTTPS traffic.
But it also allows the apps to prevent you from manipulating their DNS. You don't know when an app is ignoring the resolver you configured system-wide, because it is masked in its HTTPS traffic.
There is a worrying trend that apps (browsers especially) are ignoring whatever you configured in your system, and are becoming basically a blackbox outside your control with a wide open connectivity to the Internet. No explanation needed, what that means for any privacy left.
However if the only ISP you can get is so hostile, the solution is to tunnel (IPSEC/SSTP/whatever works) all your traffic to a non-hostile network.
That way you dont have to tunnel all your traffic. (Though technically you could also use the tunnel for only DNS, but its not much easier than the solution above if you want this to apply to all your devices)