Maybe a good approach would be to pass everything as references?

Alternatively, check what the function wants to receive, and pass in that. If the function wants a list, pass in a list. If the function wants a reference, pass in a reference.

The main reason functions get written to take references as parameters is that you can only pass one list to a function. myfunc( @foo, @bar ) will be received by sub myfunc { as one list in @_, without a way to discern the previous boundary between @foo and @bar.