I had exactly the same problem with my Simon Dillon Cinema publication (where I put all my film reviews of new releases). It should have a lovely homepage designed by yours truly, and instead manifests in Medium's uniform blandness that they seem determined to inflict on everyone. So if someone clicks on a film review, then clicks "Simon Dillon Cinema" at the top or bottom, the layout is the Medium version, not mine.

If you click "opt out" in the settings submenu, it restores the original page. However, annoyingly, it only appears how you intend if you refresh the main page after clicking on it. So unless everyone who looks at your homepage does this, they get the Medium version. Still trying to figure out a workaround. No joy so far.

One last point: If you click "opt out" you should make sure you check your tags afterwards, as Medium removed mine (Film, Cinema, Film Reviews, Movies, Culture) so I had to add them back in.