Here is a workaround, first use this one-liner to indent your use lines

perl -pe " s/^use\s+(\S+)\s+(.+)$/sprintf q!use %-20s %s!, $1, $2/e; "
+  < input > output
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then tell perltidy ignore that section by surrounding it with #<<< and #>>> and you get

#<<<  do not let perltidy touch this
use Carp                 qw(confess);
use Cwd                  qw(abs_path);
use File::Basename       qw(fileparse);
use Data::Dumper         qw();
use Digest::SHA1         qw();
#>>>
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