This behaviour of the Input Indicator is extremely annoying.

I do not agree that this is not a bug. Certainly when you are going to click an icon and at the moment of the click the icon shifts away it is a bug. The bug is more serious when you are about to double-click an icon and after the unwanted shift you click a different icon instead.

This is the only place I was able to find where someone is trying to fix this bug. I am wondering why. Is the combination of Remote Desktop + Input Indicator so rare?

I think the best solution would be that the Input Indicator icon becomes inactive (grey) when a Remote Desktop window is active.