The application switcher in Gnome indeed is designed to switch all windows of an application. There appears not to be an easy option to change the behavior to raise only the last active window of the application, except for coding, which the developpers of Pop!_OS apparently did.
Currently, this situation can be coped in one of the following ways:
Switch to the window switcher— Move to the Window switcher instead of the Application switcher. In "Settings", "Keyboard", "Customize shortcuts", look in the "Navigation" section and set "Switch Windows" to Alt+Tab, rather than "Switch Applications".
The application switcher is designed to manage windows per application. It thus brings all windows related to the application to the foreground. While application switching with Super+Tab, you still can select a specific window of e.g. the terminal only using Alt+`.
Alt+`— Allegedly, this is very inconvenient if you need to switch back and forth between one window and a specific terminal window. Then, however, Alt+Esc has you covered. It will switch between the two last windows. If you hold Alt, it will switch between the open windows without any popup.
Move to another workspace— An alternative way to cover this workflow is to move any other terminal window to a different workspace. However, there is no easy way to quickly "dismiss" a window to the next workspace: the dedicated shortcut key (Shift+Super+PgDn/PgUp or Shift+Ctrlkbd>+Alt+Left/Right) moves you along with the window to the new workspace.
Hide— A third way to cover this workspace is to hide the other terminal windows. In Ubuntu, the shortcut Super+H hides the window. Leave only the terminal window you currently need visible, and you can Super+Tab between that single window and a window of another application.
