That largely depends on which version of shintô you're talking about and whether or not you're Japanese.

If you're Japanese, then the emperor and you have a lot of shared cultural baggage regardless of how you position him within your version of shintô.

That's something you'll have to sort through and decide for yourself. And of course he ranks pretty high in the hierarchy in both kyûchû shintô and jinja shintô.

If you're not Japanese, it mostly depends on which version of shintô you practice.

If you practice one of the jinja shintô you're most likely going to have to come to some sort of accomodation with the position of the emperor in your version.

If you practice one of the many versions of minzoku shintô you have much more latitude. With no disrespect meant, he's just not that relevant to many of these practices, and you can choose to include or not include him.

From my viewpoint it just makes more sense to attend to the local first and far distant last, if at all.