It may be slightly simpler to skip the "build perl bindings for ImageMagick for each platform" step, and use the command-line magick tools. While it's admirable to try to integrate the two into a monolithic tool, there comes a point when it's valuable to rely on system() and ship a small private bundle of dedicated tools.

For example, many Mac OS X tools are starting to embed more of these tiny command-line tools into their .app packaging, unbeknownst to the user. The fact that for Darwin, an application IS a subdirectory just helps that process along, but there's no reason you can't do that with application bundles on other platforms.