I have multiple virtual desktops. Presently, Sublime Merge opens on the same virtual desktop that it was last closed on. For a simple multi-monitor setup, that is probably the right thing to do. For virtual desktops (i.e. more than the number of physical monitors), that is kind of a pain, because I have to flip through all of my vdeskops to find out where it has opened.
It would be nice to have a checkbox to override the default behavior (i.e. “always open in focused window”).
There is a setting in Sublime Text that would presumably fix this for you:
// remember_workspace makes Sublime Text remember what workspace each window
// was in last. When set to false the OS left to determine which workspace
// a window is opened in. This doesn't work with Wayland.
"remember_workspace": true,
Merge and Text share a back end, so possibly this setting might work for you.
To use it, you would choose Preferences > Edit Settings in merge and add the setting with a value of false to the file that opens (ensure that it is valid JSON; after you save keep the file open just case).