1) Don't think for one second anyone knows the best way of organising stuff - we don't. All we know are better ways than the past. Anyone who tells you they have the perfect way is talking horse.
2) Mapping an environment really helps with organisation or at least the exploration of the possible ways we might organise.
3) The use of mapping and high levels of situational awareness is a necessity for coping with evolution unless you have exceptionally talented people who understand that things evolve (i.e. they have their own mental models, can cope with inertia etc). Without extremely good situational awareness then I'd suggest you go for a cell based structure and hire rock star developers who work well with others.