There is no reason to trunk VSAN1 or any VSAN for that matter unless its actually being used.
There are some bugs out there where you need to trunk the Port VSAN, however I would not even do this unless you are hitting those bugs. For example, say the Port VSAN for fc1/1 (TE Port) is 2, so then you may need to trunk VSAN 2 to avoid certain bugs. But this is a bug issue, not a design issue.
VSAN1 is bad because its the default port VSAN. Not using VSAN1 is a good practice as this way if someone plugs in a switch and it starts to trunk, you are not introducing fabric instability and other undesired behavior.
I am pretty sure older FMs did not show the VSAN001s as segmented, (3.3), I believe later on this showed this way, and thats why I thought maybe there is a preference option to display it this way, or it may just be the changed behavior of FM.