The two houses are as distantly related as you say. The use of Uncle is to help indicate the friendliness and close bind that remains between the two houses and also the respect that Samain has for Alejandro. I'd have two young members of the two houses call each other cousin, even if they are fourth cousins or more distantly related. Samain also refers to Tovias as Father and there's a couple of extra generations between them as well. Family is important to the Seraphs and using titles that emphasise the familial ties seemed to fit them.