I am not a civil engineer so forgive me if this is nonsensical: wouldn't a 3% error margin on something that's large actually mean something though .. so the size of a space ship (that's say 200m long) equates to a +/- 6m
thats not how it works, a 3% error on a 1% fall over 200 metres would be at worst a 2.6 metres for a design fall of of 2 metres, now here is the thing with errors over those distances, they get corrected as part of the process, so over the whole distance you might end up with a total fall of 2.01 meters instead of 2.6 metres.
The designed error margin for a component is essentially the acceptable tolerance. and a deviation on the tolerance or another words the error can be represented as a percentage of the designed tolerance
In that regard, 3% error is not 3% of the total size but 3% of the acceptable tolerance.
Engineering design allow for context based tolerances, so what is considered an acceptable tolerance on one scale, is usually still an acceptable tolerance on another scale, for the same type of engineering problem.
For mechanical engineering, there are design fits and tolerances that vary depending on the acual implementation and not so much on the scale of the design.
For example a bolt embedded in concrete that a structure bolts into, usually has a starting tolerance of +/- 3mm for the bolts position and maybe a +/- 1mm tolerance for the bolts height, and often a +/- 2 thou tolerance for the bolts thread and diameter, it makes no difference if the bolt is 10mm in diameter or 100mm in diameter, those tolerances remain the same (usually)