TBH, I actually haven't used Theme Builder that much yet...but I do recall it being somewhat difficult as it doesn't allow you to actually do anything with Polaris in that tool. Theme Builder was great for visualizing the outcome...but not so great for the "associating as a variant of Polaris" part.
What I did to get around this (and successfully make a variant for Polaris), was to start a new theme in a subproduction instance in a "throw away" update set (no plan to promote to prod)...then, I used theme builder to actually build the theme as I like, visually.
Then, I created a new update set and I specifically leaned-on section 4 of KB1120004 for this next part -- here's a direct link for your convenience: https://support.servicenow.com/kb?id=kb_article_view&sysparm_article=KB1120004#section4
You'll be looking for the records that you created in Theme Builder, which should be captured in your "throw away" update set and you'll be copy/pasting the "base" and "properties" stuff, into the "style" section of the variant record you are creating.
Also, the logo used for Next Experience UI (top left) is pulled directly from your "company" record, in the platform and not actually a part of the Theme or it's Variants. I also believe that the text which comes up when you hover over the logo, is still in the "UI16 Properties" section...but the logo isn't (contrary to what it says in KB1120004 section 9).
