As you are using Royal Mail as your courier, is there any specific reason why you do not want to use buy shipping?
Apart from major bulk discount, everything stays the same, including average weight and your annual postings, as it is all through your RM account number.
Integrating your Royal Mail account into Amazon allows you to keep your negotiated Royal Mail rates and gives you the protections on your OTDR as well as VTR and a few other protections from negative feedback over courier deliveries.
All your buy shipping mail can go in the same bags as your Click & Drop mail as long as it is the same stream, ie T24 RM48 etc.
There is no need to separate Amazon mail from your other mail, just the need to download the end of day manifest for your postman to scan as well as your C&D manifest.
Although it is very maddening that Amazon have deactivated you for using Royal Mail, but will reactivate you if you use Royal Mail through their Buy Shipping settings.
Nothing has changed, same company, same staff, same network, same everything except Amazon has it run through them for whatever reason they have decided.
But unfortunately, it is their sandbox and their rules.
If you send out Amazon Prime, it is contractual for you to use Buy Shipping in order to be able to ship Prime.
Personally, i prefer Buy Shipping over C&D as it is more stable, especially at Christmas when C&D goes offline several times for hours, causing stress not being able to produce any labels.