I actually like the approach you used, where you connected the rooms together, and disavowed anything you saw out of the current room if when you actually got there it was different. I actually remember you mentioning that earlier, and was certainly one point towards me picking this game for the Maps Of The Month. Honestly! Yes, it ties into a particular cinematic event this month, but since TerraEsperZ submits a lot of good stuff that it seems like I have to recognize Terra almost once yearly, but with so much to choose from, I figured I might as well pick something a bit more interesting. This being obscure (at least to North Americans) and with an interesting mapping method (which I apparently recalled correctly) it seemed like it was a good time to do it.
I would be interested to hear what you would do differently. A full map but having bits of outside rooms might be confusing, wouldn't it?
I think what you did was fine, and is not really a "lie" because all one cares about is the playable area. It might be nice to embellish "outside" areas as a way to make a map your own. For instance, I was always thinking of trying something like taking one of the NES Mega Man maps (hi, Revned!), since they tend to be jagged lines going right and down, and filling in the empty space. Using tiles from the same map, I would complete partial structures and landscapes, until there's no empty space. For purists that just want to know what the actual map is, I would put a border around the original map, to separate it from the creative background. I think it could look really cool, while preserving the integrity of the game space. While not exactly the same as it sounds like you were doing - perhaps even the opposite (I was describing something additive, yours was probably more subtractive) - it still is an interesting question, of how to handle things out of reach to the player. There have certainly been creative things done to the map of The Legend Of Zelda: A Link To The Past, notably changing the sky/earth separation in Death Mountain, or completing the top of Hyrule Castle or the area around the pyramid.