Interesting conversation with Just Jap (BC Racing supplier) today regarding height adjustment methods. The person I spoke to agreed that the method of setting limits first then using preload to adjust height is a much better way of setting coilovers up, if you have the time, tools and resources to do it right, this includes corner weighting etc. However, the BC Racing method detailed in their instructions is OK for about 90% of their users and is not wrong, just quicker and easier.
Plus since mine were out of warranty I was free to do with it as I wanted

We also discussed some of the 'issues' I have had with the BC ER's, that is the lack of linear adjustment in the rebound and the design of the external canister limits height movement to an extent. The limit of movement was acknowledged and that was it (known issue). The lack of linear adjustment in rebound, it was suggested that on a heavier car it would be more linear and it may help to start a little higher (towards hard) than what would be 'normal'. Maybe this issue could be solved with custom valving, not sure and not discussed. However, all up a pleasant conversation with a person who knew their product and suspension in general.
Again the question is why are there adjustable collars (asked of me by somebody else) and I think that unless the coilover was completely customised for the vehicle then almost every manufacturer (including MCA) needs some flexibility to adjust the coilover length for a car. Even MCA state that the length is what they consider best (based on their testing and assumptions), however if needed it can be customised hence their method of adjustment takes in the ACTUALL car's suspension and setup.
So either way is not wrong, just one is easier than the other. It will be interesting to see how this turns out and if it is worth the effort. I have a feeling that I will have to compromise on ride height to ensure bump/droop are maximised. I'll measure everything up before I make any changes, take detailed notes, many pictures and do a write up for those interested.