I think there are a lot of valid ways to interpret it. When I was writing it I was mainly thinking about how the player might be feeling at the end of the game...
Disappointed that it's over, glad to have beaten the game, anxious to find out more details on the storyline, interested in the potential this game might have for my research, awed by the success of a game by two people in comparison to many other games I've played, eager to restart and find all treasures/secrets/song plants/recipes, sorry for Naija, but also for Mia and Eric, curious about the influence of the crystals and the spirit world, as well as the dry land...take your pick.

But essentially, there is a gap between what a writer seeks to create and what an audience will make of it through interpretation. For example, if I unleash some of the usual interpretative tools I would use, I'd say: The song has clear reference to time, which returns twice (lines 2-3,6-7), references to the journey that is past, but also one that is to come, and bending of tense (past tense in last sentence as apposed to lack of tense in the first stanza apart from "drift," present or future tense, extra emphasis on was by doubling it). Importance of repetition is apparent, two instances of lost to the waves, and the earlier mentioned repeats as well. Most nouns are emotional or related to emotion or mental processes (heart, time, lost, memory, journey ->mental process as well as physical journey), and the waves reflect both the physical waves of Aquaria and the mental waves of Naija, Mia, Li, Eric and the rest of the inhabitants (depending on the interpretation here).
Stanzaic patterns are bound by musical connotation, but two stanzas of four lines each, with varied pattern of beats, seemingly 3-3-2-2, or with elongated notes or silent beats it could create regular 4-4-4-4 song-verse.
Outside question: is this part of the Verse?
Haaah, that was fun. Say, Alec, if you are reading this, are you perchance available for an interview concerning the composition of the story?