Yes. It seems apparent (now anyway) that the code KindleUnpack extracts from a MOBI7-only ebook is really only useful for rebuilding a MOBI7-only ebook with kindlegen (if you want the output to be identical to the original). And since kindlegen creates a dual-purpose file
by default, the KF8 portion of that dual-purpose file (which will be rendered by any device supporting KF8) will be wonky and will introduce the unwanted space between the paragraphs.
After creating your three new ebooks (with Kindlegen), you could use KindleUnpack to then split the MOBI from the KF8 and that MOBI-only file will look the same as the original on all devices. But if you have any hopes of creating a KF8 file (or dual MOBI/KF8 file) for your final use, I can't recommend doing so with the KindleUnpacked source of a MOBI-only ebook. If you do, it will likely only render the same as the original on a device that
doesn't support the KF8 format.
I've probably only confused you more, but that's about the best description of what's going on that I can come up with.