I found the following Apple document on code signing:https://developer.apple.com/library/mac/#documentation/security/Conceptual/CodeSigningGuide/Procedures/Procedures.html
According to the document, you can sign a Mac app with a third-party certificate using the codesign command, so it looks like you don't need an Apple developer certificate specifically unless you want to sell in their App store, in which case you can get one simply by paying the required $100 annual fee.
I have not yet been able to find any specific information on the root certificate problem when importing an Apple developer certificate into Windows for signing Windows apps.
That's what the docs says, but if you _dont_ use an 'Apple Developer ID' certificate, Mac OS X 10.7.5 & OS X 10.8 by default will not allow your app to open. When you signup with Apple, they give you two certs, one for the App Store and a 'Developer ID' cert.