System-wide shortcut to open a new window in Safari?
In Automator, create a Service workflow (pre macOS Mojave), or a Quick Action workflow in macOS Mojave.

Add a Run AppleScript action, replacing the default code, with:

tell application "Safari" to make new document


The above piece of AppleScript code by itself will open a new window in Safari however, it will not have focus. If you want the new window to have focus then use a tell block, e.g.:

tell application "Safari"
    make new document
    activate
end tell


You can then assign a keyboard shortcut in the usual manner per information in the link within your question.