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If an engine will only produce link types that you have unchecked, it means it will not use that engine anywhere.
Rest of your questions is not handled. The engine on the further submission does not know what type of link it really is.
>if I choose "Comment-Contextual/Anchor text", will it always create contextual links in the comment too instead of using the usual Name, URL, and comments (to make name anchor text)?
Checking this will create whatever the engine and site allows. It's unknown to the program yet what will come out here.
>How do I control this type of engine, to whether post only anchor text, contextual or both?
You can't, simple disable it than.