It seems to me there are two issues with many nested transclusions,
- There is the rendering of the transcluded content
- There is the listing via filters to choose the order and items to render, typicaly nested.
When you stop to think about it, the filters are a design convenience, and help new content to be categorised, however once complete they are perhaps unnecessary processing to run each time.
- Lets face it once complete the bible should have a fixed content and structure.
Perhaps an approach could be designed so rather than sophisticated filters you just iterate static lists of tiddlers, if the static list is present iterate it, if the static list is not present then use the full filter.
- You could create a batch process to generate and store the static lists, and it may only need to be run once.
- If you have notes and annotations keep them out of this process