You should be able to upload bundles through safari. Everything in OS X sees bundles as normal files, but attempting to upload one results in "POSIX error: Is a directory".
Creating a zip file from the bundle and uploading that seems like an obvious thing to do.
<rdar://problem/3709505>
WebKit now supports a way for an application to generate a replacement file for a file upload selection. See ChromeClient::shouldReplaceWithGeneratedFileForUpload. But the actual work to allow selecting bundles and generating the replacement zip file is done in the application. So I'm marking this as "invalid", but really, some amount of support for this feature is in WebKit, you just won't see it without the corresponding support from the application.