Some notes...
Have anybody noticed this?
I wonder whether this is why Lazarus itself cannot be minimized?
I can confirm that Lazarus IDE (gtk2 64 bit) main window loses its Minimize button after opening its other windows at Debian 10 x86_64 Xfce (but not KDE).
I think this is bug/feature of LCLgtk2 (maybe qt also - did not test) apps at Xfce (maybe Xfce on Debian/clones only).
Apps at Linux behave very differently on different distros, widgetsets, DE, WM...
For example, at the moment I am at Fedora 32 x86-64 LXQt with OpenBox WM. And with this WM modal window does not fully disable its parent, it may be minimized, maximized and resized while modal window is opened. Moreover, for gtk2 (though I have not gtk2 apps other than LCLgtk2 including Lazarus here) you can switch between modal and non-modal windows (for example in Lazarus IDE or in dseligo's and lucamar's projects when you open all 3 forms).
There are many things with Lazarus and Linux... For example, I never managed Form's property Position poDefault, poDefaultPosOnly, poDefaultSizeOnly to work...