As far as converting with any program goes, that old saying holds true: garbage in equals garbage out. A lot of eBooks are not properly formatted in the first place because it seems that many publishers/authors/creators simply lack the skills and knowledge to do so. If the eBook is really badly formatted then converting it will probably compound any issues.

As far as PDFs go, they are like cat pooh. Dig a hole and bury them as deep as possible.

As far as calibre conversion goes, it does cause bloat. It reminds me a bit of the way MS Word converts a DOC file into HTML. MS Word creates a huge file with style (CSS) wrappings for nearly every word in the document. While calibre does a much more efficient job than a program like MS Word, it still creates a hellish CSS file that is in most cases unnecessary and very difficult to read.

Here is a tiny portion of a calibre CSS file:
As you can see, not the easiest thing to use. Most of us would give meaningful names to our classes. But at any rate, calibre does an overall good job of converting and the eBooks are usually very readable. It just doesn't do a good job of creating a file that is easy to modify after conversion.