Much, but not all, of what shows up in an unpacked Mobi file is often redundant or inapplicable carryover cruft (like font-face changes which involve named fonts which are not carried in any of the Kindle devices or apps).
You can safely strip out all the non-functional stuff and replace most of the hard-coded functional bits with some CSS classes and a stylesheet whether you recompile as Mobi or go on to convert to ePub.
The best way to figure out (besides trial and error experimentation) is by referring to the official Mobipocket format documentation,
such as it is, for which bits are actually functional and non-redundant to the display defaults.
ETA: Amazon's Kindle Publishing Guidelines
PDF may also be of use. IIRC they used to have some kind of appendix of CSS tags in the back which could get "translated" to the Mobi format version of HTML.