if you mean a L3 port channel supporting IPv4 and MPLS I personally prefer to use parallel indipendent L3 links.
The load balancing on L3 links should be based on the more internal MPLS label.
Increasing the mtu, mpls mtu of port-channel interface (and may be of member links) is needed.
If you mean increasing the MTU on a L2 port-channel connecting two switches this is needed too to support MPLS VPN traffic.
In this case of L2 port-channel load balancing could be based on the external label that points to remote PE (these are generally less variable then inner labels)
Hope to help