I have to agree that the Hanko is rather different. One can get one's hanko registered at city hall (and in some rare occasions it is necessary). That registers the seal, but it does not effect ones name for legal or pronunciation purposes.
As far as I am aware, non-Japanese do not have a Kosekitouhon. You have to be Japanese to have a kosekitouhon. The concept is itself Japanese, and I am not aware of its existance in Western countries. Non-Japanese can be mentioned in a footnote of their spouse's Kosekitouhon but that merely notes who their spouse is married to.
Non-Japanese have instead a passport and a Gaijin card. The Gaijin card will contain the name on the passport. And since the passport is non Japanese, it will not have kanji on it.
However, (and I am not sure of the conditions for this) one can get a "nickname/handle/commonly-used-name" tsuushou 通称) written on the back of ones gaijin card, which in my case was (changedthe card) in Kanji.