When I spoke about using your storage under a different VLAN, I should have stated that is if you had other devices that would be dedicated to talking to that storage. For your normal access to the storage server, you would use a different VLAN to communicate to it.
I tend to forget that most people do not run as a complicated setup as I do, where my servers that do a bunch of tasks like virtualization on top of the storage use the higher MTU, whereas the clients on the virtualization do not see the underlying storage because it has been virtualized. I then expose the storage virtually for desktops and servers to make use of it.
So for most using a higher MTU would not make sense to do if you are exposing your unRaid storage server directly to the client machines. If you were creating a cephs storage cluster or something like that you would want to use higher MTUs. A virtualization storage system that communicated between machines would only be via one VLAN for storage and another VLAN for external access like the Internet or management.
If you are on a flat network and will be accessing that server directly, you would never set that system up for a large MTU. Keep it at 1500.
One example for the use of higher MTU would be, something like, you have another system set up to do rsync of your unRaid box for backup to another, you could set a VLAN up for just that alone to increase throughput.
Never have used unRaid before, but if it supported a redundant system to backup to, then that would be a case as well. Your VLAN for backups or syncing would make use of it.
It is common in the industry to use a separate VLAN for backups, syncing, and other high throughput services that would never be connected via a client-side network.
Based on what you have said so far, you can set the MTU on the switch as high as you want, but set all of your interfaces at the correct MTU for use if the unRaid box needs Internet and client access.