It will work. When the daycare man says that they do not seem to like each other much, that mean it will just take a little longer to breed than usual. Its because they have the same ID.
If they have Different species, same ID numbers
The chance of getting an Egg is 19.8% (has a value of 20). The old man in the Day Care will say: "The two don't seem to like each other."
Pokemon of the different species and the same ID number do not like each other and will be less likely to breed. Just be patient and an egg will come eventually.