What pdurrant said.
When you're converting the opf with kindlegen and then viewing with a Kindle app, I think you're seeing the KF8 portion of the file--which will look very wonky and unformatted if built from mobi-only source. I think this because you just can't build a mobi-only book with kindlegen/Previewer. It always builds a combination MOBI/KF8 file. And if the Kindle App supports KF8, that's what it's going to show you.
I suggest this:
1) Take the calibre mobi (converted from docx) and extract the mobi-only contents like you have been doing.
2) Make your edits to the html and opf and then convert with kindlegen (using the opf file).
3) Take the resulting kindlebook (which is at this point a combination MOBI/KF8 file) and use KindleUnpack to split that file into its component .mobi and .azw3 files (check the "Split Combination KF8 Kindle eBooks" box ).
4) Load the .mobi file produced from step 3 into your Kindle app or the Kindle Previewer
I just checked and all paragraph indents, top margins an other original formatting were retained in this manner.
You could also go from DOCX to ePub (or DOCX to MOBI to ePub if something about the DOCX to MOBI conversion achieves a special need) with calibre, then edit the epub with Sigil and convert it back to mobi.
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