I've always felt that isometric maps can at times be some of the best looking maps, yet be the most frustrating to present to viewers. Unless the various map parts are isolated and already fit together by themselves like Solstice (NES), it's always a pain to assemble them and especially if dealing with indoor/outdoor areas and/or multiple overlapping floors.
I never got far or serious enough with Max Payne (GBA) to struggle with these issues, but I knew they were about to show up as later stages feature those exact obstacles I just mentioned.
In this case where the two outdoor areas as supposed to fit together, you *could* try and make them fit if only to save some space on the map, and link the various doors with "straight" lines/arrows. And if the doors don't align perfectly, simply have the lines change direction along the way; it would look good as long as you still followed the isometric axes.
Of course, I suspect that what would work for this level would quickly become unfeasible later on.