A regular request from customers I have seen, is that they would expect different deposit values, dependant on whether the customer is having an item home delivered, or to collect from another store.

Home delivery often requires the customer to pay in full up front. Where as collect at another store is often pay on collection.

the solution to this would be to configure the deposit value based on the shipping method assigned to the line.

Admittedly this becomes less clear on a mixed order, however the logic would still work

I have 1x Item for home delivery at $20
I have 1x item for collection at $10

If home delivery was 100% and collection was a token 10% deposit. The deposit value should be $21 - with $9 to pay on collection.