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Looking at the InDesign and calibre MOBI files I see why they're displaying differently. The InDesign file is using a series of before the entries in order to have them indented. The entity create a hard space that is not collapsable. calibre is using a series of nested blockquotes. Since, MOBI not having very robust margin support calibre fakes the left margin using blockquotes. The amount of indentation is not adjustable (aside form adding more by nesting).
Both ways have disadvantages. Blockquotes as you see have a large indent. is not going to have an indented left margin if the text wraps onto the next line. Unfortunately, I don't know how one would prepare an input document (if it's possible) to not put the TOC into blockquotes.
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