Employees may be paid in both USD and a foreign currency for example (I know this is very common for expats, getting paid separate amounts in both the local currency, and their home currency). In such instance, where local deductions are applicable, they would also need to be entered in the applicable currency in the payslip.
Employees can also incurr out of pocket expenses in both USD and a foreign currency, and want to be reimbursed in the original currency (which the company can do especially when it has the corresponding foreign currency account).
And finally, yes, some employees (or contractors treated as employees in Manager for simplicity) may be paid only in USD, while others only in a foreign currency.