Good question. I found the translation used in this example to be
inexact ["You are choosing what's good for you."]. « Qui » isn't
being used in an interrogative sense here, the phrase actually
translates more accurately as "You are choosing that which
is good for you".
The relative pronoun « ce qui » is the subject of the verb
(est), so it's not contracted.
If the sentence uses the relative pronoun « ce que », it's because
the "that which" is the object of the verb, so yes, it can
be contracted if the word that follows it starts with a vowel.
But keep in mind that the structure of the sentence would also be
different because it is not performing the "action" of the verb, so
est wouldn't likely immediately follow it.
Ex: Tu choisis ce qu'Anne a déjà choisi. ["You are choosing that
which Anne had already chosen."]