The signature of fooMethod(Class<?>) is the same as the signature of fooMethod(Class) after erasure, since the erasure of Class<?> is simply Class (JLS 4.6). Hence, fooMethod(Class) is a subsignature of the fooMethod(Class<?>) but not the opposite (JLS 8.4.2).
For overriding with instance methods you need the overriding method to be a subsignature of the overridden method (JLS 8.4.8.1). This is clearly not the case here.
Now that we have established the fact that your subclass method doesn’t override the superclass method according to the JLS, let’s look at the runtime implications when type erasure has occured. We now have two methods that look exactly the ‘same’ (same name, same parameter types) but do not override each other. If they don’t override, they must be both available on the subtype as separate methods, but they have identical runtime signatures: conflict. So Java has to disallow it.
Overriding generic parameter types using raw parameter types is allowed because raw types exist just for this reason: they are a convenient mechanism with specific unsound type rules to accommodate interaction with legacy code. So the type system here will decide that the subclass method does override the superclass one, they are identical after type erasure and we can never have a conflict. As a consequence of this libraries can be generified independently of existing non-generic code.