> Which is correct less the quote_char, and csv_quote_char, is
> this problem specific to '~' as a quote char?

As I said, I think this is a problem in the general vs. per-table setting of quote_char option.
I don't think it has to do with '~' specific char.

I didn't understand if connecting to DBI as:

my $dbh = DBI->connect('DBI:CSV:f_dir=.;csv_quote_char=~;') ...

solves your problem. For me it did...