Bozja: enjoyable lore, a GREAT start...

[Enkidoh]

Tempered altering form isn't deliberately caused by the Primal, but because they have been overtempered, namely their aetherial aspect has been dangerously pushed towards the element of the Primal in question (i.e. Leviathan's tempered such as the aforementioned Captain Madison, had their aether's elemental alignment over aspected to Water - when this happens the body itself is irrercoverably warped into an abomination).

This is similar to what happened to those unlucky enough to be caught up in elemental Flood, such as the Flood of Darkness that turned the Thirteenth into the Void (and thus birthed the Voidsent), and the Flood of Light that similarly erased most of the First (and mutated those unlucky enough to have been caught in it's wake into Sineaters). It's all to do with aether.

Also, don't forget, a Primal's whole reason for tempering in the first place is to create more devoted followers, thus increasing their power, as a Primal's power comes from faith and worship; making more followers means more worship, more worship means more power, and so it goes in a never ending cycle. This is why Primals were so dangerous.