I think that the setup you are proposing doesn't have much sense. Netflow data is already detailed enough that you can use traffic filtering by IP (source and destination) and by port (source and destination), so it is not like all the information will get mixed and unable to understand, netflow packets contain all that information no matter what the sources are, that's how it works.
That mess would only happen if you are collecting traffic from two separated subnets with the SAME IP ranges with two different netflow probes. For example, traffic from two separated offices both with 192.168.10.0/24 range. This case is quite unlikely so I don't think you need some specific setup.
Anyway, if at some point the situation comes to that scenario and answering your question, you can execute simultaneously several nfcapd listeners with different ports, but Pandora can only read from one folder (/var/spool/pandora/data_in/netflow), so it wouldn't help you that much. Only thing you could do is to have two separated Pandora FMS instances with their individual databases, not very practical.