Not all custom theme customizations are currently effectuated in the unified interface (as described for D365CE in this article: LINK)
As far as I have noticed, the issue concerns the following elements, which are not displayed in the right colors, despite having published a custom theme:
- Main color.
- Link and button text color.
- Page header fill color.
- Panel header fill color.
The missing functionality has been confirmed in the post (LINK).
This feature is strongly needed in order for us to be able to rebrand applications according to our clients requirements.