> In Emacs -Q there is not this issue.

This indicates the issue is with your config.

I suspect it can be from theme.

Are you sure there is no config editing org-level-* faces somewhere?

> (set-face-attribute 'org-level-1 nil :inherit 'org-default :height 1.5)
> (set-face-attribute 'org-level-2 nil :inherit 'org-level-1 :height 1.4)
> (set-face-attribute 'org-level-3 nil :inherit 'org-level-1 :height 1.2)

Also do note height work as an increment from inherited value. It does
override. So according to this config org-level-2 height will be 1.4x
times that of org-level-1.

> When I evaluate (describe-face) on any headline level, it consistently reports that it is org-level-1.
I assume you are calling it interactively (via M-x), this gets
completing-read and allows you to select. Maybe you got only org-level-1
and selectec it?

Try this,