In relation to this question about the "fundamental" character of possible logical systems, I realized that I just had an intuitive (and so, inadequate) understanding of the way logics higher than FOL can unambiguously specify the kind of semantics which make up the intended interpretation of their formalisms, inside the formalisms themselves. This is quite a meaningful question, since the ability of an automated system of reasoning at the object-language level can only recognize what is coded in the formalism itself, at that level; and so, those approaches which start from the construction of a model at the meta-level, are a priori ruled out in the sense I'm describing here.
What I'm thinking about are computer systems reasoning with the logic, such as the HOL-based proof assistants, as Isabelle.
So, how are the intended semantics of SOL and HOL specified in a computer system?
P.S. : I have realized that this topic isn't actually new in this site, and has been brought up in other questions like this one.
From the point of view of derivability and syntax, there is no distinction between full higher order semantics and first-order (Henkin) semantics. This is, in one sense, the reason that there is no completeness theorem for full semantics - because the completeness theorem matches derivability with Henkin semantics, and so any genuinely different semantics will not match up with derivability. Syntactic things like proof assistants, which only care about derivability, are somewhat indifferent to semantic issues.
I believe that the main benefit of using higher order logic in proof assistants is that it makes it easier to formalize theorems that have been proven in ordinary mathematics. Even if these theorems could be formalized in, say, Peano arithmetic, by creating entirely new proofs, it is often easier to modify the existing proof to work in higher order logic.