Does the following translation make sense in Spanish? What would be the appropriate translation?
How many more apples does John have than Phil?
¿Cuántos más manzanas tiene John que Phil?
Firstly, "cuánto/cuánta/cuántos/cuántas" is an adjetivo interrogativo which, as all adjectives, must agree with the noun it qualifies — "manzanas", in this case.
Secondly, the adverb "más", if paired with some kind of quantifier, is generally placed after the noun:
¿Cuántas manzanas más necesitas?
Necesito tres manzanas más.
Then I wouldn't separate "más" and "que" because that makes it more difficult to parse.
Summing up, I'd say:
¿Cuántas manzanas más que Phil tiene Ali?
You can also say:
¿Ali tiene cuántas manzanas más que Phil?
The last one sounds clunkier to me, but it could sound natural if pronounced with a different intonation. I would pronounce the first one with a falling intonation, and the last one with a rising intonation (or a "less falling" one), as though I wanted the addressee to complete my sentence.
Of course you could go with a different wording:
¿Cuántas manzanas más tiene Alí con respecto a Phil?
I don't love the last one, but that is personal preference.
In light of the English grammar involved, to make it similar of what a Spanish speaker would say, I'd phrase it as:
¿Cuántas manzanas más tiene Alí que Phil?
So it's perfectly idiomatic.
Swapping we get another sentence given by fedorqui:
¿Cuántas más manzanas tiene Alí que Phil?
I remember saying this wording once, but now it doesn't click on my ears, so I'd use the first one.