Ah, I see - the checkbox called Contains Names in the add new column dialog.
I'll need to test it out but it looks like it'd mean everything has to have & instead of comma which I don't think will be too intuitive.
Using the hack of a vertical bar sounds reasonable and would only require a little bit of explanation. So if I import a book with the collection name "LN, FN" and "Mystery" I store it as "LN|FN, Mystery". And if the user manually edits the column they need to put "LN|FN" or "LN| FN" as in "Smith|John, Mystery" so when I export I always convert "|" to "," (as long as its preceded by a-z to avoid issues with prefixes used for sorting on the Kindle) so the collection name looks right on the device. Shouldn't be too many if any Collection names with | in them that aren't a prefix. And I can restrict it to comma separated text fields since it'd be of no use in a plain text field. Great suggestion