No conversion_options is not intended to replace command line options. Generally speaking, overriding conversion options in a recipe is a bad idea, it should be avoided in all but extreme cases. And the conversion_options are being used in your case, the resolved conversion options in the debug output are resolved before conversion_options is applied. This is one of the reasons it is bad idea to use conversion_options.
If you find it difficult to edit command lines, create a script and edit that.
None of the options you are using have anything to do with processing of <pre>. In fact, other than fake margins all the other options are heuristics options which are turned off anyway unless you pass --enable-heuristics.
And the html will always be different since it is parsed, converted to XHTML cleaned up and re-written.
IIRC old MOBI does not support <pre> though I may be misremembering, convert to azw3 or EPUB.