rRk = sqrt(x_k^2 + y_k^2)
rTk = sqrt(x_k^2 + (y_k-L)^2)
rRkD = simplify(diff(rRk,t))
rTkD = simplify(diff(rTk,t))
The swap in sign is irrelevant. This is true in mathematics:
a - b = - (b - a)
Well, it is true and always has been, unless something has changed in mathematics. However, you never know with the new math these days, and some boards of education.
As for a dot derivative form, MATLAB does not provide that form. It is purely a notational thing, so why do you feel you need it?