It seems this is a better solution:

body {
    @apply(--paper-font-common-base);
}

Just to make sure:
Did you put your :root selector inside a <style is="custom-style"> as mentioned in the docs ?

Yes I did. (otherwise none of them would work IMO)

I'm not able to reproduce this issue. For example, the following works fine:

http://jsbin.com/narasahace/edit?html,output

I've also tried this directly with paper-styles and don't see the issue. Can you provide a test case that shows the issue? Thanks.

Please note that the custom-style that uses --paper-font-common-base must be after the import that defines the variable, in this case paper-styles\typography.html.

It turns out the other line I put before @apply seems to be the problem. Reordered the lines and the problem seem to be gone.

Here's an example: http://jsbin.com/lehutolebi/edit?html,output

Thanks. We've tracked this down and it should be fixed in the next release.