My son has cf, autism, celiac disease and numerous food allergies. I have been cooking 2 separate dinners for 10 years. You do get used to it. Most times dinners are completely different because my son has so many limitations and the autism makes him refuse a lot of foods he can have because of textures.
i do sometimes cook him up some meals on a Sunday and freeze them. But I know that isn't always an option. For things my son can eat like chicken, I will leave the skin on his and remove the skin from everyone else's, then season the way they like. I have to be concerned with cross contamination for him, so I use to separate pans. Mashed potatoes for your son would be great. You can load them with butter and salt while masking baked potatoes for everyone else. Veggies are easy everyone can have them, just pull some out for your son and add whatever he wants to add calories, while leaving the rest for everyone else to enjoy. This is what a shared meal looks like at my house. This is as close as we can get to everyone eating the same thing, and it really isn't anymore work than cooking one meal.
As you continue to need to cook this way, you will find ways to tweak your menu so everyone can enjoy and have what is best needed by their health needs. I would think because your son des not need to avoid any particular foods due to allergies, you could adjust just about any meal to keep everyone happy and healthy.
Something else I do is when my son really enjoys something, I make extra for him for the next evening. Then I can make something for the rest of us that I can not tweak for him, like lasagna. Everyone has a dinner they will enjoy, and I only cooked one meal.
I know it is very overwhelming at first and seems like it will be time consuming. But with a little pre planning, it's not so bad. It will become your new normal and will just become automatic for you. Good luck.