Hi @Mr_Wood,
I was just playing around in "beta" because my institution does not apply different branding/themes to different (sub)accounts. We also do not have a complex sub-account heirachy.
While look at settings for my root account, I came across the "Let sub-accounts use the Theme Editor to customize their own branding" setting. We have it not checked.
When that setting is not checked and I go into the settings for any sub-account (including any sub-accounts under another sub-account), "Themes" did not appear on the left-side.
When that setting is checked and I go into the settings for any sub-account (including any sub-accounts under another sub-account), "Themes" does appear on the left-side.
I applied a different theme that I quickly created to one of my sub-accounts under another sub-account. After doing that, as I switched from one course using the original theme to another course using the new theme, my I saw the changes.
If you are not able to customize or are not experiencing what I have tried to do and describe, there is probably something unique your permissions or (sub)accounts or entire instance.
Have you reported this directly to Canvas Support so that they can look at this with/for you?
-Doug