There's a big difference between recovery pain and chronic pain. Also, if someone has joint pain, they are doing the wrong exercises. For example, running trashes my knees, but biking does not. Also, picking up heavy shit (weights - squats and deadlifts) is the only thing that resolved lower back pain (from sitting all day).
Doing anything more than you should will trash something in your body. How much of something you should be doing? Pain is a good indicator. I you are below 40 you shouldn't feel it at all. If you are above, you should feel it a bit and observe it closely while reducing the load. If it gets weaker with time, you have appropriate load, if it doesn't or gets stronger, your load is still too high.
Everybody has bad everything. We are walking wrecks about to fall apart in few short decades. But there's genetic variety. There are dozens of variants of genes that code something as essential as collagen. Some resulting in very crappy kind. Some really do have it worse. That's why everybody needs to be listening to their bodies and apply themselves accordingly.
I’m in the same exact boat with deadlifts helping my back pain from my desk job.