Yes, font-size works on small-caps.
Since this is just for your own personal use on a device that supports font-variant:small-caps then there is no reason NOT to use it...if that is the style you are looking for.
Sorry, Jon, but making everything lowercase and then small-caps defeats the purpose of small-caps....which is to differentiate between upper, and lower, case letters but using the capital style of the letter.
Code:
THIS IS SMALL-CAPS
THIS IS UPPERCASE IN A SMALL FONT-SIZE OR LOWERCASE IN SMALL CAPS
Just type (or leave) the text with normal capitals and lower case where you want them and apply the font-variant:small-caps to the phrase.
If you were worried about distribution of the ebook and widespread compatibility...then small-caps isn't supported very well and you would need to use some of these work-arounds.