1) I'm not sure if there is any benefit to using a plugin if it is pure php code. Why not just use require_once()? The whole advantage of plugins over a standard require_once() is that it will deconstruct a full page and break it into it's component pieces... updating necessary links and other references and then place it into the correct corresponding location on your page. If it is pure php it wouldn't know whether that code belongs in the head or the body, so you would have to place it manually to the correct location.
In your case you could still use it, but you would want to delete the header and title references from the page that are automatically placed, since you aren't using them.
It probably is a bug though. Technically they should all three be blank and you should have to refer to the ->Contents of the plugin to return a result since there is no head, body, or title defined. I'll log a bug to get this fixed.
2) Remove the meta information from plugins where you don't want it added... you could also remove the head reference and instead add the css and scripts individually as well as just the meta from the plugin that you want to actually use. In order to keep it simple we include the entire head, which will include meta information if the plugin page has it. If multiple plugins have meta information, there is no way to prioritize which should or shouldn't be used, so it would have to be a human decision at some point. It seems the easiest route would be to simply remove the meta tags from plugin pages where you don't want or need them.
I will log a feature request to add a binding for "Header without meta" and to ask if you want to include the meta information when applying each plugin. This would allow you to make that decision during application more easily instead of having to remove the meta tags from the plugin pages beforehand.