It isn't pointless, particularly in newer versions. In those (6.0 and later, I think) you don't have the ability to store VM's on the boot data store.
The boot subsystem isn't technically on a datastore. It contains additional partitions that steal space that would otherwise be available to a datastore that may or may not be created in the excess space available on the boot device. If your boot device is USB, it will not create a datastore and the USB device is used exclusively for the boot environment. If you use the default interactive install, it will create "datastore1" in the spare space on the boot device as long as it isn't a USB device (i.e. SSD, HDD, RAID).
I realized having the ESXi itself on one disk and the VMs on another is most probably pointless, and I would like to migrate that together.
The problem is, ESXI is on the smaller SSD and the VMs on the bigger one (128 vs 256GB). For endurance purposes (but this might be pointless concern on a microserver with five VMs max) I'd like to move the system to the bigger SSD. How would I do that though? Is there even any simple solution?
Moving the system with ESXi isn't supported. The system is installed on its own set of private partitions, and if you have an existing 256GB SSD with a datastore on it, you would have to delete the dataset, install ESXi on that SSD, then recreate the dataset (slightly smaller).
You can potentially
save your ESXi configuration and import it back into the new ESXi image.
However, I have to say, overall this is a nontrivial exercise in reorganization and I don't suggest you do it.