Your cover problem is because Calibre is probably set to Add a cover (and Jacket) and did not detect that there was a 'cover'
In EPUB both the PAGE and the IMAGE must get the Semantics set to cover
IMHO Dropcaps are always iffy once they hit a device (blame those devices for variations on following a CSS). In this case, the Calibre viewer is also a device that does not match the 'Word viewer device'
I use the editor to code for my devices. Yes, the same code does NOT perform as desired on both my Kindle and EZReader. I fine tune for the targets.
If you are targeting the Public, You will need to make versions for each or KISS (very simple layout)
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