This answer is based more on the interpretation than on the rules as they are written. The first thing to note is this:
The homunculus is friendly with you and your companions and obey your orders.
The second thing to note is this: the mental statistics of the alchemical homunculus are …
Int: 10 WIS: 10
For comparison purposes, these are the same mental statistics that a communist possesses. This means that your Homunculus is about as intelligent as a typical human being.
So, you have a tiny and flying construction that is about as smart as a typical human being and that obeys you to the best of one's abilities. This makes it significantly smarter than a familiar (the smarter has Int: 3).
So, yes, I would certainly say that it strongly supports the idea that your Homunculous can understand how you "signal". In fact, I said it strongly supported the idea that a Homunculus could be given and executed without problems. In terms of "difficulty", if a random player could understand how to do what your homunculus tries to do, he should also be able to understand it.