That's mainly how I do it, too.
A word of caution, though: if you're using the contents of the mobi8 folder (created by mobi_unpack) to reconstruct your MOBI using Kindgen/Previewer, you're building the joint MOBI/KF8 file from only the KF8 portion of the source. Meaning that if you originally created a joint MOBI/KF8 that uses media-queries to manage (compensate for) the incompatibilities between the two formats, you're going to lose the original MOBI 7 portion (I mean it will be built using only the KF8 side of those media-queries, not that the MOBI 7 portion won't be
there), when you rebuild the mobi8 folder contents
Because of that, I rarely use the mobi_unpack output to rebuild the ebook (unless it's something really simple where there were no media-queries involved in the original). I mostly use mobi_unpack for inspection and then return to the original to make the changes.
I realize that the original being an InDesign project might hamper that ability to return to the original source, though. Does the ID plugin include the "source" as part of its final product? If so, that's what I'd return to change/rebuild. But I don't even know if the ID plugin utilizes the media-queries (behind the scenes) to tweak any differences between the two portions of the joint file—so this could all be moot. The bottom line is, of course, if you're happy with your workflow and the final output you're producing. Then keep doing what you do.