*** Update ***
The issue with my tenant not displaying company branding as it used to was due to a bug in the interface. Microsoft have now rectified that and I have access to company branding as I once used to.
It seems that the requirements to configure Office 365 company branding have changed. The official documentation is here:
which says:
License requirements
Adding custom branding requires one of the following licenses:
- Azure AD Premium 1
- Azure AD Premium 2
- Office 365 (for Office apps)
However, I definitely know this wasn’t the case until very recently, because a tenant I have without Azure AD P1 or P2 that allowed company branding configuration and now does not. So, something has indeed changed recently and I can find no acknowledgement or documentation of that. The existing branding of the tenant remains unchanged but I can no longer make changes.
If you don’t have Azure AD P1 or P2 in your environment you can always sign up for a 30 day trial and make changes. However, after that 30 days ends you’ll need to buy a full Azure AD P1 or P2 license it seems, if you wish to modify the company branding it seems.
I would have thought that in a world where we want to make tenants more secure using something like branding to help reduce the risk of phishing attacks tricking users into putting their details into false portals, the ability to brand a tenant would be available to all licenses.
Hopefully, this is simply an over sight by Microsoft and the ability is returned. However, for now it appears they are fully enforcing the licensing when it comes to company branding and requiring an Azure AD P1 or P2 licenced user to make changes.
CIAOPS 
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