You do not tell us what Xojo versions you are using. (plural)
The feature was added in:
48185 IDE On the Project Chooser dialog you can now select a recent item and press back delete or forward delete to remove an item.
Now, you said they come back ?
I saw wizardry when I use different Xojo IDE versions.
But, I suppose that if you use 2017r2 or later only, you will not experiment that.
Nota: my latest license is for 2015r1. And, when I fall into trouble, I load my project with the current (to date) version to check if this still exists (if so, usually, it is my bug).
I hope this help you.
I also use Recent Projects to open a Project folder in the Finder (so I open the project and Cmd-Click in the window title bar to open the project). Then I can reach the information I want, whetever it can be (last project version and other stuff).
No, my Xojo projects are not all stored in a single Xojo Projects folder; they can be anywhere they fit best (often because I have data I use within the project - Drag and Drop for example).