1/ If you start editing with the Rich Text editor, change your settings mid-editing then save your draft, the generated HTML will instead be saved as the text of your chapter.
(The workaround is obvious (don't change edit mode while writing/editing a story), but I thought the case should be known.)
This is known behavior. (Though it might be convenient if CHYOA would determine the editor used and send that information when the chapter is saved.)
2/a) Despite being syntaxically identical, the first two nestings are wrapped in a paragraph (with blank space betwen outer list and inner lists), while the third has only a line break.
That's weird indeed.
It might be related to a bug in the Markdown parser, though it doesn't happen in the environment, so I guess it is a bug that has been fixed in the meantime.
Though it is possible to work around it.
The structure needs to be like this
Code:
1. **Header 1**
- Indented Line 1.1
- Indented Line 1.2
1. **Header 2**
- Indented Line 2.1
- Indented Line 2.2
1. **Header 3**
- Indented Line 3.1
- Indented Line 3.2
with two spaces before each -
(In all cases but Line 3.1, you could omit the leading spaces and it would still work. Though it might break in other Markdown parser implementations.)
For additional indention, you need another 4 spaces in front of the line like
Code:
1. **Header 1**
- Indented Line 1.1
- Indented Line 1.2
- Increased Indention 1
- Increased Indention 2
- Increased Indention 3
- Increased Indention 4
- Increased Indention 5
The conversion from RTE to Markdown syntax doesn't work out for every Markdown command, so you might need to use plain Markdown (deactivate RTE) to use these formatting options.
(As already has been pointed out: Please don't save a chapter with a different editor setting than it has been opened with.)
Unfortunately, the Markdown specification isn't unambiguous so editors-to-Markdown converters and Markdown parser might use different approaches and thus create results that might not be predictable.
For the next version, we might go for an editor and a parser that both meet the CommonMark specification that would allow for an unambiguous syntax interpretation.