Nightmist Manor has an 'SI Safe' teleport-to-house that apparently checks somehow if you're 'supposed' to be in the Isles or in Cyrodiil, and if you're not, flips the bit to the correct setting for where you're going. Could you do something similar for the teleport to the tower, if you're coming /out/ of the Isles?
Alternately, you could just disable the teleport to tower while in the Isles, but it'd be a lot more convenient if you could just zip across the realms both ways by having both mods installed.
Nightmist Manor mod for reference: http://www.tesnexus.com/downloads/file.php?id=29609
Lavish Mage Tower mod for reference: http://www.tesnexus.com/downloads/file.php?id=29609