Do Tracking Categories affect how Budget Checking is applied to requests?

Yes, Tracking Categories do have an effect because they are a filtering option.

If you upload a budget for a specific Tracking Category, it will be applied against the line with this Tracking Category+Account. 

Please note: The overall budget, which is set without Tracking Categories, will be applied to both: items with and without Tracking Categories (because in this case, there's no filter set for a Tracking Category):

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