To answer your question, it is a little of both.
The reason hot rocks are frowned upon more than UTHs and basking lights is because they fail to spread heat as much as the previous. To feel the effects of the warmth, the animal will need to sit directly on the rock. Since reptiles dont have the nervous system we do as humans, it is harder for them to tell if they are getting injured (especially on the belly) and many reptiles will get burnt from sitting on the rock all day.
You may think that a thermostat can circumvent this but this is a little tough to implement. The heat mat/ tape is on the outside of the cage so if there is a malfunction with the thermometer there is at least a little buffer zone between the heat source and the reptile, where the hot rock is in the cage with no buffer zone. Also I cant really think of a way to securely attach a thermometer to/around the rock so the reptile cant disturb it sans tape and glue which can be bad for the reptile. You can have the same problems with a heat mat which is why owners should check this often, but the lack of buffer zone between a heat source and reptile is the biggest concern. One problem that can happen with mats is the snake crawls through water then goes to the mat and the water heats up (with a higher specific heat it is harder to heat but when it is heated it loses heat slower) and that can harm the reptile. Now with a mat you have some form of substrate so the snake would need to burrow for this to happen, but with a rock it can happen anytime they go straight from the water dish to the basking spot.
That being said, many of the rocks are also pretty poor. A lot of hot rocks have "hot spots" which means they have spots that are hotter than the rest of the rock and this can mean even with a thermostat on the rock certain spots can be warmer than the rest of it. This is not as true for high end heat rocks, though. I have seen newer ones with build in thermostats and auto shut off features because of the bad rep they have, but why would you get a higher end one of these when you can just get a UTH or a bulb? In many cases the UTH or bulb are a lot easier to set up and a heat rock should only be used after careful observation for a long time and things like surge protector and a higher end rock. I have heard of people building a little cage around the heat rock and that probably would work but like i said it doesnt spread heat as much as a bulb so that seems like a lot of wasted effort to me. Also why risk the health of your snake for it when people have obviously had problems with it?
All of the above is talking about an electric heat rock, but the same principles can be applied for a rock heated by a ceramic.
TLDR; the rock is hard to heat evenly and the hot spots can injure your reptile and the rock being inside the cage can injure your reptile MORE than other heating sources
