Is there a way to prevent Yakuake from opening when the currently-focused application can use that shortcut instead? e.g. The default shortcut is F12, which VSCode also uses. So when VSCode is focused, I have to close Yakuake to be able to use F12 within VSCode. Is there a way around this or do I just have to use a different shortcut?
Are you asking how to remove a conflict of 2 programs using the same shortcut?
Yes, break the conflict and change one of the shortcuts.
I can recommend using alt + ยง (button below esc, to the left of 1) for yakuake, easy on the fingers and nothing else uses that shortcut.