Personally, I have never seen that, but I suppose it could be possible. What type of boa do you have - species and morph?? Some darkly pigmented boas may have some gathering of pigment cells in odd places such as in the mouth.
However, I would check him veeery carefully to make sure this isn't mouth rot. You could take him to the vet, but you could take a look yourself. Have someone help by holding him for you and hold the head (hopefully your helper is experienced holding snakes still). Use a q-tip and insert it sideways into the snakes mouth very gently. Once you have it between his jaws, move it at an angle (up and down) to open the mouth so you can examine the spots more closely.
I know you said there was no obvious discharge, but once you have the mouth open, look for discharge very closely and for any "cheese-like" substance. if you see anything like this (other than a normal amount of clear saliva at the back of the throat) or if the spots look lumpy, schedule that vet appointment. If the spots truly look like spots of coloration within the skin, he should be fine. I would continue to monitor and examine the spots in this manner every few weeks to look for any changes though. Just to keep an eye on them. Anything out of the ordinary with them would warrant a trip to the vet.
**If you have another helper who can take some pics of this exam, please post them!!!
Btw, to google some additional information, look up "stomatitis" and "mouth rot" in snakes. Warning - graphic pictures!
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