Hello.
We need to look at your supply in two separate parts.
The first part of guidance you refer to in your example is for the sale of goods from Amazon to the end customer.
As Amazon is accounting for the VAT on this transaction it would be excluded from your flat rate calculation.
The second part of guidance regarding the zero-rated deemed supply relates to the goods that you have imported into the UK and then are deemed to be supplying to Amazon.
The purpose of this is to allow a business to reclaim the import VAT they may be incurring on bringing the goods into the UK.
Zero rated supplies are included in the flat rate scheme calculation.
However, this scheme may not be appropriate for your business as you would end up paying VAT on a supply where you have not charged VAT and the flat rate scheme would not allow you to separately recover the import VAT.
A business may leave the flat rate scheme whenever it wishes please refer to notice 733 section 12 :
Leaving the scheme