If I have a page that is declared in the header: INDEX, FOLLOW
The page will be indexed and the links will be followed. Actually it's almost redundant this tag on a page you want indexed, just I am at the mercy of a 3rd party plugin that won't remove it. So.
Then further down the page there is a canonical URL that says, actually SE SPIDER you should go an index this other page because the one you are on only has a few things which are different from the one you are crawling, so best index that one.
The fact that the index,follow is in the header isn't going to confuse anyone is it? I am currently reviewing some SEO on a website and want to make sure I am drawing the right conclusions even if they defy logic.