The overlay opacity should change during scrolling while holding down the ctrl/cmd key. But if the shortcut key isn’t pressed, then it shouldn’t.
I’m afraid touch gestures can be a bit awkward, subject to exactly what computer / input device you are using (which is one of the reasons why they can be turned on/off – sometimes they are just quite frustrating). For example, on a Mac I might turn scroll gestures on if I am using a Magic Mouse but off if I’m using another kind of mouse, since they send QuPath different kinds of input notification. Some devices support scrolling left-to-right as well as up and down, while others require pressing shift to achieve that effect.
I’m limited in the range of devices I can test, and I’m not even sure it’s possible to access all the required information to fully support different devices in Java. Therefore I expect there isn’t an easy fix, and it is a matter of choosing which preferences are most comfortable for the devices you are using.