Can you test lactose tolerant genetically but still test as intolerant on a food allergy test from the doctor?

Yes, especially if the result is CT.

The ’T’ allele is the lactose tolerance version, and the ‘C’ allele is the intolerant version. Individual's who carry the T allele should produce enough lactase, but in some cases they feel symptoms. Discordance between genetic lactose tolerance and the good doctor test (something called an HBT, hydrogen breath test) can signal a secondary cause of lactose intolerance such as Irritable Bowel Syndrome. There are also some other things that could be causing it rather than just lactose - for example they could be allergic to casein, the protein in milk.