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I really like Spreadsheet Compare, but I've noticed that it doesn't handle well a situation where there are extra columns of data. I realize it can get tricky to recognize when a column (or several) is missing, but I wonder if you could key off the Column Header Row when the "Worksheets are databases" selection is chosen; if the header cell name doesn't match, you search ahead to find a match and then adjust the matching of cells accordingly.
I realize this is a nontrivial change, since it means creating a list of columns to skip, and then you're not matching column numbers between the two spreadsheets. I'm sure it's less needed than properly handling missing rows, which SC does well in my experience. But it would be a beneficial enhancement for me, and I suspect for others as well. (My need is to test output from an application, and with enhancements to the application, sometimes there are new fields of output, not always at the end of the row.) I would think you could use the same kind of code you used for missing rows.