The tolerance is a percentage of the total linear measurement.
Yes, absolutely, I could not have said it any better. Another thing Dcox is that errors do build up - you might start out with a piece that is .01 or .03, but when that is glued to another piece, then those pieces have some tolerance errors too. If you want that kind of accuracy, then (not being sarcastic - but being real here), you will need to keep your calipers very clean with alcohol or acetone to keep the mating surfaces of the calipers clean each time you measured a part.
Let me say it this way. In the "machinist world" there is no such thing as perfect. Everything has a tolerance to it. It also depends on what you are wanting to achieve. If we had an example of a process you are trying to do, then I can be of better guidance. You said something about a superstructure, usually when modelers refer to a superS, they are talking war ships or other 'structures' within a very large ship that has many decks or layers to it. For instance the Bismark has superS as well as the Titanic.
I personally think perhaps you should lower the bar of expectancy for yourself just a little bit and enjoy your project - I admit that this is hard for me to do as well as I like for things to be 'just right'. Plastic medium is much easier to achieve than wood by far. Metal is even more precise to work with as I can remove .01mm of material off some stock if I have to. That is 1/100 of a mm. I think that is less than a human hair (maybe)?
So, I am not going to say one way or another 'if you are anal or not' - that is not for me to be critical, but I will say that overall, I think that is too much to ask of yourself and the main thing is to stay within 'reason'.