It wasn't really clear to me that using Qt::CTRL | Qt::ALT is still part of the usage. With that, the problem makes a lot more sense.
Qt::Key_R | Qt::CTRL | Qt::ALT evaluates to (Qt::Key_R | Qt::CTRL) | Qt::ALT, which results in QKeyCombination | Qt::ALT, which is what's raising the warning, since QKeyCombination does not have any (non-deprecated) operators itself.
Qt::CTRL | Qt::ALT | Qt::Key_R instead evaluates to (Qt::CTRL | Qt::ALT) | Qt::Key_R, which results in Qt::Modifiers | Qt::Key_R, which is an operation that is defined.
This is kinda the answer I was looking for.