I had the same problem and I've solved it this way:

## no critic
package My::Package;
## use critic
use strict;
use warnings;
[download]

so that Dist::Zilla::Plugin::PkgVersion will expand it to:

## no critic
package My::Package;
BEGIN {
  $My::Package::VERSION = '1.23';
}
## use critic
use strict;
use warnings;
[download]

and everyone is happy :-)