Hello, my name is***** and I have over 20 years of experience as a veterinarian.
A change in skin color can be from irritation (secondary to itching, or a yeast or bacterial infection), ultraviolet ray (sun) exposure, or endocrine imbalances such as thyroid or adrenal gland function abnormalities or if he isn't neutered, secondary to sex hormone imbalances.
If his appetite is very good, he's drinking lots of water and he has a "potbellied" appearance then adrenal gland disease (hyperadrenocorticism) is possible and should be tested for with either an ACTH response test or dexamethasome suppression test.
If he has weight gain, poor skin and haircoat health, and lethargy hypothyroidism or low thyroid gland function is possible. It is important to check a full thyroid profile, not just a T-4 when looking for this disease process. A T-4 can vary greatly throughout the day and thus isn't an accurate total picture of thyroid health. The level may have been taken at a single high point making thyroid gland function look normal, whereas the rest of the time it may be significantly subnormal. The Michigan State University laboratory does a terrific job with their thyroid profiles.
If he is not neutered then sex hormone imbalances may be the root of his problem. Sex hormone levels can be checked to determine that.
If his skin feels greasy or oily and there is hair loss a secondary skin infection may be involved. Yeast is most common but bacteria is possible too. A skin swab cytology will help to determine that.
But if he seems perfectly normal, with a normal coat over the area that is spotted, and his skin simply has spots that seem darker in color (they can be gray or liver colored) then he may just have more pigment in those areas, and this is no cause for alarm.
If you have pictures of the areas I would be happy to take a look.
Please let me know if you have any further questions.