One issue is that subheads are sometimes used in the spec without a numbered subsection above them. That is, hierarchy levels are skipped. Possibly the best solution is to remove subheads from the bookmarks altogether.
We should decide also if links to tables and figures should appear in the bookmarks within the chapter links. This is unconventional, but possibly useful. On the other hand, given that the bookmarks contain a link to the Table of Figures and Table of Tables, in which each figure and table is listed, users should easily be able to find figures and tables.