On Windows, launch QGIS. You get an icon of the application on the task bar.
If you hover over this shortcut, you get a preview of the QGIS dialog
Open some print layouts or other modeless dialogs. At some point, instead of a single QGIS icon on the task bar which, hovered, would show preview of all the print layouts + modeless dialogs + main dialog of QGIS, you can get a second icon on the task bar.
This sometimes makes switch among dialogs hard since you have 50% of luck to get the item you want to open.
Open a new instance of QGIS and things become awful to manage: you can get a new icon on the task bar for this project, or you can have this new project preview accessible through the existing icon or the main dialog is shown in the first icon preview and some of its print layouts are shown in the second icon preview or the reverse.
It's a real mess: you are never sure whether the icon you are going to click will allow you to access the dialog you want to use. When you have two projects that look alike, you are never sure of which project refers the print layout you just moved to.
I think that a QGIS instance should add a single icon on the task bar and all the dialogs I'll open from within this instance, should be previewed/accessed using that single icon. If a new QGIS is opened, then it should create its self contained icon, like the previous one.
Windows 10, tested with 3.9 but this is an older issue.
This issue persists on versions 3.16.14 and 3.22.1, all projects and layouts still stack together making it harder to easily select the project/layout intended.
I think that a QGIS instance should add a single icon on the task bar and all the dialogs I'll open from within this instance, should be previewed/accessed using that single icon. If a new QGIS is opened, then it should create its self contained icon, like the previous one.
Windows 10, tested with 3.9 but this is an older issue.