I like that they think of security, but this is the type of thing that forces people back to X11. Their own screenshot tool does not adhere to the same workflow, so maybe they are blind to the issue.
Considering that Gnome is now the default DE for the more popular distros, I doubt Flameshot will ever receive the honor of becoming the default screenshot tool, even though it should. It provides most of the capabilities that a user would need when taking a screenshot. Desktop Linux needs these little goodies, so it can be sold to the average user.
Given the level of integration between KDE apps it's unlikely they will prefer an outside tool either.
This is indeed very frustrating.
Something related is in the works for screenshares, a "remember this decision" option. https://feaneron.com/2021/11/13/adventures-with-portals/ At some point maybe something similar will come up for screenshots.
On a related note, GNOME Shell 42 should have a nice new screenshot integration: https://thisweek.gnome.org/posts/2021/12/twig-24/#gnome-shel...
Which isn't surprising, in the least. I agree with aidenn0, if you're using a custom screenshot tool, you're not using GNOME as it's intended to be used.
Here's another fun fact, their music player doesn't have a volume control and that's how they think end users should use it.