So... the issue is quite simple:

Urkan CAN'T go on water if you got the boat tech UNLESS you finish up the research while they are unrooted ^^ (I have no idea if that work while they are under someone else control)
I think it's quite a bug.

An Urkan that got the ability to go on water because he was uprooted don't loose it once it root itself.

Also, the Urkan that are on an ice shelve while they disappear bugout...

Can confirm, here's a save with Fakir tamed near water to the right of my main city, shipyard is 1 turn away from completing

Urkan embark bug.sav