Small caps are typically reduced in size a small degree. When processed through calibre, the font size is changed to next smaller size on the scale. As you noted, that makes small cap paragraph starts looks dispraprotionatly small. You can, however, customize the scale that calibre maps font sizes onto.
When Converting, in the Look and Feel section, look at the Font Size Key. Try changing to this one instead: 10.5, 11.0, 11.5, 12.0, 13.5, 17.0, 20.0, 22.0, 24.0
(Note that when I convert from AZW3 or Epub, I prefer to disable font size rescalling entirely, unless the books needs it.)
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