By design, the drives mount in the drives folder located in /var/hda/files. Since you made your first drive mount in that location that is why it's in the storage pool.
You can mount drives pretty much anywhere you want. The only requirement is that the mount point exist, i.e. folder before you mount. So if you want to mount your drives as /var/hda/files/drives/drive1 and drive2 then the folders must exist there and have the correct permissions.
By default, the hda-diskmount script on ALL Amahi versions mount drives in those locations. You can manually change it of course, but must unmount the drives the remount in the desired locations as you indicate in /etc/fstab.
The wiki has a lot of good guidance, but it does not tell you to mount as /var/hda/files. It states you can and describes how, so it's your decision where you mount the drives. Having it mounted in the storage pool is not a big deal in my opinion, but I am no expert. If doing so causes a problem, then I would like to know the reason.
If you don't want drives mounted in /var/hda/files/drives location, then I suggest you pick a different location. Just remember that the Greyhole LZ needs to be in a location with sufficient space. I myself have a 200GB partition assigned as /var/hda/files and that serves as my LZ as well. In my case, it's sufficient. May not be for yours.
what I am currently doing to solve this for myself is this:
I have added a 500GB USB drive to the greyhole storage pool as /var/hda/files/drives/drive3
I then used:
# greyhole --going=/var/hda/files/gh
to tell greyhole to take this drive safely out of the storagepool
its now running a #greyhole -fsck
to make sure everything is ok.
when it finishes I will take the drive out of the storage pool in the greyhole.conf file.
reboot and see if all my shares and files are still there.
then format the drive into one big partition and add it as /var/hda/files/drives/drive2
that way my storage drives will be nicely ordered as drive1, 2 and 3
will probably remove the 500GB USB again from the pool after everything is OK.