I think the intention is "yet", but with software projects like this it can be difficult to be certain. However the Windows version has been receiving a lot of attention so it looks promising.
To work around this problem you could try generating the epub from Scrivener an then editing that in Sigil to change the TOC. You can then generate the mobi from the epub using free software from Amazon (which may be part of the Scrivener install, I haven't looked at the recent versions).
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