(No) Indenting is not a
problem, it is a preference
I believe Calibre uses the current default conversion preferences from the GUI for the conversion formats specified. So set that to your choice.
Fixing already converted book is fairly easy.
Find the style applied to the indented paragraph:
Use the Calibre ebook-viewer. Right-click on the paragraph and select inspect.
That will show the class affecting the area and the style sheet settings for that class (inc inherited).
Use Tweak-epub and a text editor to change text-indent: <your value here>