To address any "fix" in the authoring file you'll be wanting to open a converstion about your problem over at the InDesign user forum.
Alternatively you can remediate the PDF (using Acrobat XI Pro).
Working in the PDF's structure tree you'd do the appropriate tweaks.
Alternative give Toru a try (move low numbers to a higher number position).
Use working copies. There is no "undo" when working in the structure tree / TORU.
I doubt InDesign will ever change its behavior in this regard - too many complications…
In any case: when it comes to ceating accessible PDFs per the app;icable ISO standard (PDF/UA - ISO 14289-1) the reading order (in the sense of sequence of objects in the page description) is not relevant any linger, rather the reading order (in which content is to be presented to the user) shall only depend on the order reflected by the tagging structure.
OK Further investigation I found the inline boxes are in order its just the custom anchored boxes that are not respected. So inline all good. Custom more work in acrobat to re order.