What is the height of a 'containing block' when you're device uses auto-scroll and doesn't have pages/screens??
1% of a 5000 word chapter would be a mighty large top margin...
(and yes, I know there aren't many 5000 word chapters...that was a slight exaggeration for illustration purposes)
I agree with jhowell that the 'vh' size would be more correct, but jswolf's 'small em' would be a better second choice... IMHO