When you set up a booking extra you need to decide where the collected money is going to, owner or the agency.

You set this up under Properties > Booking extra > click onto the name of the booking extra.
There are four different variation to allocate the collected money of a booking extra.

1) A set amount is being paid to the owner. The rest is paid to the agency.
This can be used to pay the full amount to the owner or only a portion of it.
In the owner payment tab this would like this:

2) 20% of the money + VAT is going to the agency. The rest is allocated to the owner.
In the owner payment tab this would like this:

3) This setting is not very intuitive, but is means that the whole amount is allocated to the owner.
In the owner payment tab this would like this:

4) Again, this is not the most intuitive of setting, but it is a fast way to allocate all money of the booking extra to the agency as commission.
The amount is showing as gross in the owner payment tab. In the statement the VAT is itemised. Using the -1 would not do this.
In the owner payment tab this would like this:

The -2  setting, in combination with selecting a supplier (owner) to whom the money is to be allocated, is allowing you to keep easily track of all the booking fees collected. Inculding having the VAT itemised in the owner statement.
Supplier is somewhat of a misnomer in this case though, as it is an owner that needs to be selected.

The owner needs to be selected in the Supplier column.

This will create a separate payment section at the bottom of the owner payment tab, showing that the whole amount has been allocated as "commission".
Though in this case is not really a commission.