I think there is an example of using Custom Specials for this in the community files as well, for the Noble Class, if I remember correctly. They get 1 or 2 class skills they get to choose.
On second consideration, these three classes do they always get the same # of class skills? If so you could make a class special and bootstrap that X number of times at 1st level, have the class special choose among all skills, and pull the ClassSkill tag to the special. Then push that to the linked class to give it the class skill.
For example, if the Arcanist always gets 4 class skills, bootstrap the special 4 times, each of which chooses a skill, pulls the tag, pushes it to the class via the linkage.
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