You say you prefer an external USB drive so you can rotate it off-site with an alternate.
I'm looking at AirPort Admin Utility v.6.3.1 connected to a 2 TB Time Capsule firmware v. 7.7.2
Actually there's a feature in the AirPort Admin software under the Disks tab to "Archive Disk...". The sheet that drops reads as follows.
Are you sure you want to archive the AirPort Time Capsule disk to a disk connected using USB?
Destination: <pop up>
Make sure the storage device has enough space for the archive before connecting it to the base station's USB Port.
So it looks like you can use the clean form of the internal drive on the new Time Capsule and bring in your external drive for the occasional backup then take it off-site again.