Ah the JL lemma. Probably one of my favorite too. I'm teaching a mathematics of data course next semester, and even though we don't assume probability as a prerequisite I'm going to find a way to talk about that idea.
So it needs judicious care when used along with algorithm s that work with inner-products
That's trivially untrue. You can move the origin around and that doesn't change the el_2 metric but will change the inner product.
This would not happen for random rotations of course because they do not change the origin. However random Euclidean motions can change the origin.
The popular proof does uses random linear transforms and they indeed will not change the origin, but that's just one class of transforms with the JL property.