Terminology for types of universal computation
The key words you should search for are "naming systems", "representation", "notation", "numbering", ...

The usual concepts of computability are defined over strings (either unary which is usually stated as $\mathbb{N}$ or binary which is state as computability over $\Sigma^*$ where $\Sigma = \{ 0,1 \} $). (They can be extended to $\Sigma^\omega$ but here I will stick to the countable case.) A model of computation is called universal if it is Turing-complete (i.e. it can compute any Turing computable function).

If we want to talk about computability over other sets, then we need a naming system. A naming system for $M$ is a partial function from $\Sigma^*$ onto $M$. If we have two sets $Y$ and $M$, and a naming system for each of them, then we can talk about computability of functions from $Y$ to $M$. 

One can define a partial order over naming systems of a set $M$. $\gamma \leq \gamma&#39;$ iff some computable function can translate $\gamma$-names of objects in $M$ to $\gamma&#39;$-names of them.

Let me give a simple example. Assume that $M$ is the set of Turing machines, and $\gamma$ is one of the common ways of encoding Turing machines as explained in computability/complexity books. Let $\gamma&#39;$ be defined by adding a bit to the names telling if the corresponding TM halts. Then $\gamma&#39;$-names can be translated to $\gamma$-names by a computable function but not vice versa. $\gamma&#39;$-names contain more information. If fact, we we can solve the halting problem for Turing machines if we use $\gamma&#39;$ as our encoding.

Obviously we don't want to have non-computable information coded inside the names of objects as above, so we use names which have the least amount of information in computability (assuming that they exist). (In complexity, the complexity of a problem can depend on the naming system that is used for the inputs, and different naming systems can be more suitable for different purposes. There is no least if we change the requirement for translation from being computable to say poly-time computable as is shown by padding arguments.)

After defining the computability over other sets using naming systems, one can talk about a universal model of computation over them w.r.t. fixed naming systems.

Now, if the names in a naming system contain non-trivial information, then it is not very interesting for a machine to be universal w.r.t. that naming system anymore.

For further information:


Yuri L. Ershov, Sergei S. Goncharov, Anil Nerode, "Handbook of Recursive Mathematics", vol I and II, 1998
Klaus Weihrauch, "Computable Analysis", 2000