A "Service Charge" G/L Account line is marked as a "System-Created Entry" (field 101 in TAB 37). And in the current design System-Created Entries are excluded from prepayments.

That means that a customer gets two documents and need to perform two payments, even in scenarios with 100% prepayments - one prepayment invoice for the goods and then the final invoice with the service charge. 

A "Service Charge" G/L Account line (coming from "Invoice Discount" table) should be considered for prepayments like any other G/L Account line which is added manually to a sales order .