They can be under a general perk tree. While perks have skill requirements, that does not mean every perk has a skill requirement. So Jump, carry more, sprint faster can all be under a general tree or a everyman perk list.
This is actually an extremely important question, not just in regards to acrobatics and athletics. Imagine how many "general" perks that can be added by modders if they are NOT necessarily forced to be tied to a skill. Assuming for example that mounts are in the game, there could be a variety of riding perks in the general category, that otherwise have no logical place.