Yes, it should help you skip the check but you might get "unpredictable" (or rather uncomplete) results from these calls.
The reason being that before the container is validated, there is no way to make sure that the whole set of beans is present and therefore that BeanManager#getReference will return a correct result (the bean might not exist the moment you call it but would exist later on).

You should rather seek a way to alter your application to avoid this call.

It says that it skips this kind of checks, but not sure what kind of side-effect I'll have in this case.

Difficult to say without knowing your application. Better try not to use that mode or try to figure out in how many places you bump into similar problems.