The functionality you describe is exactly what is provided in the 1.4.1 release.
The only caveat is a issue with any existing VSANs DomainIDs on your UCS system that fall into the range of 3840 to 4078. If you attempt to enable trunking and have VSANs in that DomainID range you will receive a warning that those VSANs will become disabled. If you proceed, they will go disabled and no longer pass traffic. All other allowed VSAN DomainIDs will continue to function properly.
This is a recent changed that was introduced with the MDS NX-OS 4.1 code. Which the UCS shares with at 1.4.1 for fc trunk
Regarding your question regarding what VSAN to put the end ports into. As you'll be starting in NPV mode, it's best to ensure proper connectivity by having the UCS and MDS end ports in the same VSAN. This will establish the link up properly and eliminate later physical level troubleshooting.
In UCS, trunk is disabled by default, see above for reason. Enabling UCS trunk mode is at the switch level, all uplink ports will be trunk enabled. In the MDS trunk mode is enabled at the interface level (individual link or port-channel). Once trunking is enabled on both sides, all VSAN from the UCS side are allowed. The MDS side can be trimmed to allow specific or a range of VSANs. Default on MDS is all VSANs.
As to what is best practice for what VSAN to put those end ports into, is a subject to debate. My best practice is to use VSAN 1, as VSAN 1 can never be deleted, which means the SAN port-channel will never lose it's native port.
