At some point we will provide a means to apply conditional CSS – CSS that only appears on certain pages. Conditional CSS will probably be rendered inline in the <head> of the document. While I’m working on this feature, I would be happy add an option to specify that styles should be added only to AMP pages. In which case, the styles would be inserted between <style amp-custom></style> tags.
Right now we’re working on improvements to the targeting options however, so it will be a little while until this feature is added. But it’s on the list.