Warning. This is an attempt at an answer out of curiosity rather than an expert answer.
Newton has the following passage in "Recomputation of surfaces of least resistance," (1694) (see Whiteside*, pp. 470-471):
Unde $aabb - 2aabx+aaxx+ bbxx = aay + xxy$
[capiendo fluxiones]
$- 2aab\dot x + 2aax\dot x+2bbx\dot x =2x\dot xy + aa\dot y+xx\dot y$
Whiteside (ibid) writes: "The dotted letters in immediate sequel are Newtonian fluxions; that is, $\dot x = \frac {dx}{dt}$ and $\dot y = \frac {dy}{dt}$ where t is some independent variable of ‘time’."
I'd like to add that I don't think that interpreted in the context (whether historical or modern), something like $x=x(t)$ (say in parametric equations) or $y=y(x)$ (say when** $y$ represents the distance from the $x$-axis at a certain $x$), would be an "abuse of the notation".
*The mathematical papers of Isaac Newton Volume VI 1684-1691
** I am pretty sure I have seen something like this in historical texts, but I couldn't remember where.
