I don't think anyone would be able to distinguish il l'a fait and il la fait phonetically.
In spoken French, the pronoun il is often reduced to a single [i] so both sentences would be pronounced the same way:
Il l'a fait → Y l'a fait → [i.la.fɛ] or [i.la.fe].
Il la fait → Y la fait → //
On the other hand, a ...
[fə.zɔ̃] is the usual pronunciation in France. Faire has a highly irregular pronunciation. The letters ai are pronounced /ə/ in :
the nous form of the present indicative.
all the forms in the imperfect indicative.
In this other answer @Gilles explains that this strange pronunciation might have its origin in the fact that in the 17th century the people ...