Firstly, that sucks and I'm sorry you're sometimes in pain and feel concerned! Secondly, I'm wondering if you have contacted a medical professional about your concerns. It might be more challenging to go into the doctor's office as it would be without a global pandemic, but is there a primary care provider you could give a call to and ask if it's something they would be worried about?
Everyone's bodies are different. Some body parts are more sensitive than others, and it isn't abnormal for your glans to be sensitive - like you said, the skin on the glans is thin and more reactive since it's exposed less than, say, your hands or feet. That being said, if you're in a lot of pain, I'd reach out to a medical professional about it - some conditions, like phimosis, cause tighter foreskin than is comfortable which can cause more hypersensitivity in the glans. You might want to see if that sounds like something you're dealing with.
I'm not sure if your glans being exposed in the way you describe will cause desensitization over time. Some people with penises have experienced desensitization after masturbating in a specific way and needing to increase the pressure or method of masturbation in order to feel stimulated, but can take breaks to try and increase the sensitivity again. Penis sensitivity can also decrease with age, so it's tough to pinpoint one reason someone might experience desensitization.
If you're in pain when your glans touch your underwear and don't want to be, it might not be a bad idea to introduce some stimulation to your glans to help them feel less sensitive when they are in contact with your underwear. Does that make sense, or sound applicable for you? This could look like applying coconut oil or warm water to the glans regularly.