Did some testing and I think I know where the problem is.
Looks like Calibre generated MOBI (or perhaps MOBI in general) doesn't like margins (and presumably other measurements as well) given in cm. I have manually edited stylesheet in EPUB and replaced all margins given as 0.5cm, 1cm, 1.5cm by 0.5em, 1em, 1.5em and so on - and the conversion result was close to what I expected. Sure, em and cm are not the same thing, but that was the simplest way of testing the idea. Unfortunately, living where I live and using local Windows version it would be quite difficult to not use cm.
I have a gut feeling cm were treated as inches previously, which was why these margins looked so large.
Looks like the conversion will be much more time consuming than expected :/
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