particle は - が in subordinate clauses

Since you can't use は in subordinate clauses, it looks to me like が is forced to take on both roles, so how would we distinguish them? For example, if we have the sentence

僕が好きな動物

how do we distinguish between "animal that I like" and "animal that likes me"? Since it's が, I think that if we treated that clause like a sentence on its own it would definitely mean "I am liked" since が would directly link 僕 to だ, but I've seen sentences like

彼が好きな寿司

translated as "sushi that he likes", so either my assumption about が in a full clause is wrong or the way it works changes somewhat.

So far I've assumed that you can use clarifying nouns like 方 or こと, but I'm pretty sure that that won't happen in every usage case, if I'm even right about that.

Thanks!

Answer

僕が好きな動物 actually can mean both, the animal that I like and the animal that likes me. But to mean the former it often becomes 僕の好きな動物, and to mean the latter it often becomes 僕のことが好きな動物 or 僕を好きな動物. In reality, you wouldn't run into such ambiguous phrases frequently.

But when you do encounter phrases like 僕が好きな動物, its interpretation purely depends on the context and your common sense. I am a native speaker of Japanese, and recently posted a wrong interpretation of a sentence due to this ambiguity. (There was not enough context, and the sentence could make sense either way.)

Of course, 彼が好きな寿司 almost certainly means sushi that he likes, and 寿司が好きな人 almost certainly means person who likes sushi (unless you're talking about personificated Mr. Sushi).

In this case, if there were no context at all, I feel 僕が好きな動物 is likely to be taken as the animal I like, and 動物が好きな僕 is likely to be taken as I, who like animals. Maybe it's simply because talking about 僕's preference is more common in conversations.