Just don’t minimize the window. Removing a window from the alt-Tab list is basically the only reason to minimize it in the first place on Mac. (Not reflexively minimizing windows does take some time to get used to if you’re coming from Windows, admittedly.)
you can use workspaces for that. for comparison, gnome on linux doesn't even support minimizing windows any more. you move windows/apps that you don't want to use right now to a different workspace.
On Windows there are applications that minimize to the tray instead of remaining on the task bar. That’s my most common reason to minimize, so that it disappears from the task bar when not in use.
i have used WindowMaker but also the original NeXTstep for years, and WindowMaker's integration with GNUstep apps and its emulation of the NeXTstep interface always felt incomplete.