Welcome to the community! I like your approach, it’s thoughtful and clearly tailored to how you want to work in Obsidian. That said, it’s helpful to keep in mind what JD is fundamentally about: a system for identifying and locating folders where work gets done. The classification into areas and categories is intentionally coarse to keep the structure shallow and flexible. For more on this, see this post on headers by @hans.
Regarding headers: these are meant for special cases where you know in advance that you’ll have no more than 10 headers and 10 items per header. Beyond that, headers carry the risk of requiring re-indexing, so I would advise against using them extensively.
As for using JDex-style IDs for area and category folders: strictly speaking, it’s not necessary for location and retrieval. But your decision seems well thought-out, especially to address aesthetic and technical needs in Obsidian. So in that context, your adaptation makes sense.
If you’re starting from scratch, I also recommend checking out this thread for a smart alternative approach to organizing standard zeros and area management: Alternative layout for the standard zeros
On cross-area references: JD encourages placing each item in a single, clearly defined location, based on where it’s most actively used. If something belongs to multiple contexts, consider using links or tags.
One final point: I’ve found that I tend to overcomplicate the JD structure. But I’ve come to appreciate that Johnny Noble’s approach is the result of years of practical use. He deliberately avoids adding more complexity than necessary, prioritizing ease, speed, and low-stress organization when storing and finding your stuff.