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I'm looking for an alternative to the ruinously expensive InDesign, which I switched to after FrameMaker/Mac was abandoned by Adobe, despite the promises it made.

I see from the feature table that Mellel doesn't do autonumbering in the style 1, 1.1, 2, 2.1, 2.1.1, etc. Ok, but in my discipline papers often have numbered lists of examples grouped in sublists, in the style (1a), (1b), (2), (3a),...

tab(1)tab a. ...
tab b. ...
tab c. ...

tab (2)

tab (3) tab a. ...
tab b.

etc, where the alphabetic characters line up, of course. xrefs in the text are in the style (1a), (1b), (2), (3a),...

Can Mellel do autonumbers and xrefs like this?

Sorry, the auto numbers are in the style tab (n) tab letter, the xrefs in the style (1a), (3b), (25), etc.

Yes, Mellel can handle autonumbering setups like that with no problem. Look into the Auto-Title feature of Mellel; you can mix and match numbering schemes, choose which level of numbering to display (even omitting a level if you choose) and also insert any free text you wish around the numbers, including tabs. (Coupled with a paragraph style for your Auto-Titles, you can then determine where you want your tabs to be located, or even choose a different paragraph style—with different tab stops—for different levels of your numbering.)

One thing to keep in mind, though, is that each level of your numbering scheme needs to be independently defined.

You can also modify the numbering style that is used for lists. In that case, look into the List Styles and review the options therein.