I do not see any inconsistency or incompatibility between supporting legacy MOBI formats and supporting newer MOBI formats developed by Amazon. Indeed, Calibre already supports Amazon's K8 format (AZW3). Therefore, I do not understand why you mention the need to support legacy MOBI files as it does not seem to have any bearing on my inquiry.
As I have verified, and documented above, Calibre ignores the existing MOBI NCX when converting to EPUB. I've tried converting a MOBI with an NCX to AZW3 and then the AZW3 to EPUB, but the resulting EPUB still did not have an NCX. Calibre includes an NCX in the EPUB only if I try to tell Calibre how to construct it.
I hope you will reconsider. As it stands now, if I want to convert a MOBI (or AZW3) with an NCX to EPUB for subsequent editing in Sigil, Calibre either creates and EPUB without an NCX, or I have to try to tell Calibre how to build an NCX. It seems silly that Calibre can't simply parse the NCX from the input file and reconstruct it in the output file.
Thanks for your attention and for your Calibre program.