Of course, microcement can be apply over a countertop, the important part is that the base, if its wood or DMF, should be completely waterproof. If the countertop is made of two pieces (because its length is too much) the joint should be stable.
Marble, stone, granite, a countertop made of bricks and cement can be use as surface for microcement.
Once the microcement coating is completed over the countertop, the only cautions that must be taken are the same that you would have with a wooden countertop should not be used as a cutting board and avoid placing hot pots or pans directly on the microcement.