I can't answer specifically for their reasons but the general reason for things like this is regulations and compliance. There is a whole pile of compliance and regulations depending on your company and industry and funding and all kinds of nonsense you have to go through when engaging with companies outside of the US or employing people outside of the US. Some industries and companies never have to worry about it but others they might have to worry about it and some definitely have to worry about it. So it is oftentimes easier to just lump everyone together and say you must be in the US or you must be a US citizen. Then the compliance regulations can get a lot easier.

From [1]

What if we incorporated as a non-US corporation?

If your company is already incorporated somewhere other than the United States, Canada, Singapore or the Cayman Islands, in order to participate in YC you will need to create a parent company that is in one of those jurisdictions. The existing company will then become a subsidiary of the new United States, Canada, Singapore or Cayman parent company.

Many companies in each YC batch do this process in order to join YC. While we will connect you with lawyers who will drive this process, it will require a significant effort on your part.

[1] - https://www.ycombinator.com/faq