VAT Question - regarding Travel Agent Activities

 Scenario is Travel Agent has now got a new european accommodation supplier who issues invoices with VAT at 5%.

When a product (accommodation) is sold, as far as my understanding goes, customer should be issued a VAT Receipt as he/she has been charged a VAT. Obviously that receipt has to include a total VAT paid by the customer so that if it was business customer then they can claim back the VAT. This travel agent has been issuing receipt with applicable VAT (currently 20%).

On VAT Return travel agent was showing all VAT received from customer in sales and all VAT paid to supplier in purchases. So in total travel agent pays VAT only on the commission. 

However in this new situation, Travel agent is confused: two possible solutions neither of which are preferable to him:

1. travel agent has to show on the VAT receipt that there are two different levels of VAT charged (ie. VAT charged by supplier + VAT charged by travel agent) in which case the customer will know what level of commission travel agent is charging.

2. travel agent continues to show the total 20% VAT and take the loss on the difference on the VAT. 

Travel Agent does not intend to go onto TOMS scheme purely because then each customer would be able to find out his commission levels. (if VAT shown on receipt is X amount, his commission would be 5 times X).

Any suggestions are most welcome. Thanks in advance.