The simplest way to record a VAT-only invoice is to create one with two lines - work out the net £X on which the VAT you’ve been charged would be 20% (i.e. the VAT total multiplied by 5), then make
one line for +£X at 20% VAT
one line for -£X at 0% VAT
That should leave the invoice total as zero net and the correct VAT amount.
Just to add to your suggestion, HMRC gave this answer:
"I would recommend doing whatever works best for your software.
As it is an import with VAT being charged and passed over to your courier then there is an entitlement to recover it and so would appear in box 4 and box 7 of the VAT return ."