I'd keep the R720xd (it's what I'm using for my FreeNAS system, though I'm running it on bare metal), get an appropriate HBA card (I'm using re-flashed H200s), the appropriate SAS cables (I bought Dell M246M x 2), and put 8 10 TB drives in RAID-Z2, buy a spare 10 TB drive and burn it in ahead of time, and put 4 SSDs in a 2x2 striped mirror. Get that all running and pour the data from the existing FreeNAS server over the new server at your leisure. Then do whatever you want with the old hardware. Plex is fine in a jail IME, but if you have ESXi, you could equally well boot Plex from an iSCSI volume on the FreeNAS guest like you do the other VMs. Put them all (or mostly) on the 2x2 SSDs.
Complications: you need to boot ESXi from somewhere and that somewhere can't be from the HBA (which is entirely passed through to FreeNAS guest). I'd probably boot ESXi from an internal hard drive [doesn't need to be SSD if it's only running FreeNAS], pass the entire HBA through to FreeNAS, and boot FreeNAS from a VMWare volume. In this setup, if either ESXi or FreeNAS crap the bed, you lose all your machines, so consider whether some of your machines [domain controller, print server, PBX, pihole, and UBNT admin] should be ESX guests with storage on the ESX internal drive so you can reboot FreeNAS as needed without losing services.
Alternatively, you could periodically snapshot your VMs (especially if ESXi "knows" how to checkpoint with FreeNAS) and back those machines up to the physical hard drive every so often. That way, a FreeNAS outage can be alleviated by launching VMs from the physical hard drive, but they spend most of the time running off the 2x2 SSD array over iSCSI.
I would not punt on the 720xd, but I also would not pass through only select drives; pass through the entire HBA. You have some on-board SATA (and an internal onboard USB in addition to the external USBs). I'd use those, or even use an additional RAID card or HBA for ESXi [though you don't have a ton of mounting options inside the case for non-hot-swap drives for ESX]. 128GB is a great start. The 720 motherboard has plenty of RAM slots for later expansion if you need it.
