nCr and nPr: Order of Operations Parentheses, Exponents, Multiplication, Division, Addition, Subtraction.
Where would a counting concept like nCr and nPr fall into this mix?

There is no strong convention for these notations.
In most cases the $C$ and $P$ notations are self-delimiting, because the arguments are typeset as subscripts or superscripts. They can be written as ${}_nC_r$ or ${}^nC_r$ or $C^n_r$, where in each case it is unambiguous that the argument expression is whatever is written in smaller type -- or as $C(n,r)$ where the parentheses and comma make the structure explicit.
There are a few cases where ambiguity does arise, such that if you write the functions as ${}_nC_r$ and want to multiply two of them. In that case it is strongly advisable to use parentheses to disambiguate rather than try to rely on a convention: $({}_aC_b)({}_dC_e)$.
In any case, in more complex situations it is often preferred to use binomial-coefficient notation $\binom nr$ instead of ${}_nC_r$, and that is completely self-delimiting. The counts that are written ${}_nP_r$ in some elementary combinatorics texts appear to be rare enough in advanced material that it is generally feasible to write $\frac{n!}{(n-r)!}$ for them.
