Yeah, this is an interesting question.
が doesn't always refer to the subject in ~ほうが. For instance, in a sentence この家は駅から近い, the subject is 家, and 駅 is obviously not the subject. However, が is attached to から in the structure for comparison; この家は駅からのほうが海からよりも近い. Similarly, 談話室 is the location, not the subject, in your example sentence (嵐の音が談話室ではっきり聞こえた。). In fact, 嵐の音は談話室のほうではっきり聞こえた can convey the same meaning. (が sounds more natural, though.)
Confusingly, ほうが is not always preferred. に can't be replaced with が in an example sentence 彼女は英語よりも数学のほうに興味を覚えているようだ, i.e., 彼女は英語よりも数学のほうが興味を覚えているようだ is not used. I can only say "it's case by case". (I've read a linguist also says that he can't find any regularity when が can be used and when can't in this comparison structure.)