Is it really necessary to place the appendices in a book in the order in which they are referred to, or is it possible to have a "logical" order, i.e. place them in an order which would be chosen when the Appendix would stand alone? For example, Appendix G referres to another appendix, which logically would be placed as Appendix H, but because the reference appears so late, that appendix would end up as Appendix Q when placing the appendices in the order of references.
I would have no problem putting appendices in "logical" order. An appendix is referred to out-of-context or out of order anyway, so what difference does it make if your footnote sends the reader to Appendix A, Q, or IV?
I work at a small company doing R&D work on electrochemical process development (electropolishing, electroplating, etc.), and do a lot of writing as part of the job. A lot of projects require regular submission of reports, usually either monthly or quarterly. These reports are usually relatively short, running 6-20 pages or so. In some cases, we have a large body of data or other ancillary material we want to include that is well suited for one or more appendices. In short documents like this, I usually sequence the appendices by their position of first reference in the text, as the small scope of these documents lends a more "figure-like" feel to their appendices.
I would probably be inclined to keep the order-by-first-reference sequence up to about 40-50 pages or so of length. Above that, I'd feel more free to use a topical sort order like you indicate. In fact, now that I think about it, I used exactly this topical sort order in my Ph.D. thesis, which had seven (*gulp*) appendices, all of which are absolutely ordered by topic, and not by first reference.
Really, once the appendices section becomes substantial enough, it almost becomes its own mini-chapter. When considered from that angle, structuring it so that it has a natural topic flow is quite sensible.