Even if you fix the issue with h2xs, you'll still have to worry about actual differences between 5.6 and 5.005_03. For example, you may write a script that uses %b in a printf format; that will work on your development server in 5.6, but when you roll it over to your production server it will fail in 5.005_03. (Something very much like that happened to me because a production server had an older version of the DBI module than the development server.)

Your development environment and your production environment should be as similar as possible, to minimize the likelihood of problems arising only after code is rolled over. Personally, I would recommend using 5.005_03 on your development server as well.