In the paper linked to, there appears to be only a single primitive relation, written $x\leq y$, of which $y\geq x$ is just a notational variant. The equals part of the symbol is present because $x\leq x$ holds for all $x$ (theorem$~1.2$) but this is just a mnemonic device without formal implications. The negation of the relation $x\leq y$ is $x\not\leq y$, and it is written like that to remind the reader that it only affirms the absence of the relation $x\leq y$, not the presence of the relation $x\geq y$. In fact $x\not\leq y$ does imply $x\geq y$, but that is only shown in theorem$~1.4$.
Equality is not an explicitly mentioned relation (at least it seems so scanning rapidly), and so there is no reason to introduce $x>y$ as as shorthand for $x\geq y\land x\neq y$; for this reason theorem$~1.4$ is formulated the ways it is. But of course the hypothesis $y\not\leq x$ does exclude the possibility that $y$ actually is $x$; indeed the notation $x>y$ is introduced just after that theorem. However I do not agree with the given motivation "Theorem 1.4 means that the the surreal numbers are totally ordered", because they are not even partially ordered, merely preordered. In view of theorem 1.2 it is what I would call a total preorder (not sure the term is in use), a relation in which every pair is comparable at least one way, possibly both ways.
This is the next point; the paper states that $x\leq y\land x\geq y$ is not only possible when $x=y$. It introduces the relation $x\equiv y$ for $x\leq y\land x\geq y$, and given transitivity, this is an equivalence relation. What is really totally ordered is the set of equivalence classes for this equivalence relation.