I have been using pause work for a little over a year now and I’ve found that it’s done nothing but help my lifts. I can see where your line of thinking might be coming from though.
Pause work is to mainly focus on the isometric aspect of the training. Research has shown that isometrics building strength in a 15 degree radius of the position you are in, so using this in sticking points can be very helpful. It also teaches the body how to stay tight in certain positions (look at how weightlifters use pauses during certain aspects of their pulls). Teammate Jennifer Petrosino also is a huge advocate of this (mainly through triphasic work).
I think if one specifically did nothing but train the isometric or pause aspect of the lift and didn’t perform the whole lift at all, this might happen as that’s the only quality and position you are training. But I train the whole lifts on my speed days and with different variations for this reason. Basically I’m just trying to increase my time under tension for the areas that I need it in most.
In the grand scheme of things, the pauses probably make up less than 5% of my training. So with that said, I don’t think it’s going to teach my body to « slow » down there, especially when I do speed work where I am blasting through that point numerous times per week.
As for the stretch reflex, it should not have an effect here as it is strengthening that range of motion/point and actually probably increasing the tendon strength (the tendon is forced to hold a force and time under tension on the insertion is drastically increased). Again, I think if the qualities of the whole lifts are still trained you won’t lose any elastic effects. You might actually increase them by building thicker and stronger tendons. (Think about the tendons being a rubber band. If you use a thicker rubber band, you’re going to get more elastic strength by being able to use more of that potential energy they store.)