Yes. This is just another case of an intersection indexed by a set - here, fixing $i\in I$ the indexing set is $$J=\{j\in I: j\ge_bi\}$$ so that we're looking at $\bigcap_{j\in J}S_j$ or $\bigcup_{j\in J}S_j$ respectively. This really has nothing to do with the partial order.
I suspect the point at issue is that we initially think of unions/intersections as happening in some order. While this framework is satisfactory at first, once we move into more advanced topics it's really essential to forget the idea of ordering our sets entirely and just think about intersections/unions of arbitrary families of sets. (That said, note that things are a bit weird if we try to take the intersection or union of no sets, but this is an edge case you can ignore at first.)
EDIT: to address the comment below, yes, this is fine. We often abbreviate something like $$\bigcup_{j\in\{x: \varphi(x)\}}A_j$$ with $$\bigcup_{\varphi(j)}A_j,$$ so e.g. $$\bigcup_{j\ge_bi}S_j=\bigcup_{j\in\{x: x\ge_bi\}}S_j.$$ This is completely unambiguous and quite common; it's analogous to something like $$\sum_{1\le i<j\le n}{i\choose j}.$$