I had in a trouble like this situation.
in fact, I couldn't solve this problem.
In ProductImpl.java, there is explicit definition on additionalSkus - "SkuImpl.class"
So It can't switch our new entity automatically.
But you can solve it irregular way. (this way may illegal or violate to license, I don't know)
Make ProductImpl.java in Admin / Site Project, Same root package and Same Class name.
It would be override original BLC's ProductImpl.java.
You can refine additionalSkus's info.
Look like below.
@OneToMany(fetch = FetchType.LAZY, targetEntity = CustomSkuImpl.class, mappedBy = "product", cascade = CascadeType.ALL)