This is about the Custom Window Frame and Right Hand Menu appearance option. Mailspring gets the number of buttons correct for the other 2 window options.
I’m happy that you use native buttons here on Gnome. However all 3 buttons are only used on Ubuntu. Other Gnome distributions like Fedora and default Gnome have only 1 button, the close button. This is actually the Gnome philosophy - only have 1 window control.
Can you add an option not to display the minimise/maximise buttons when running on Linux?
A more automatic way would be to read the current setting from gsettings (org.gnome.desktop.wm.preferences). the button-layout entry contains the data.
on my system it is ‘appmenu:close’ (1 button)
on an ubuntu system it would be ‘appmenu:minimize,maximize,close’ (3 buttons)