Rice's theorem vs Turing completeness
Your misunderstanding is:


  'sure' in the sense of being computationally verified by an algorithm


We are not, and we can not be . The question,


  Is this given Turing machine $M$ a universal one?


can not be generally and algorithmically decided for the reasons you state.

However, we can prove for a fixed Turing machine that it is universal -- and that is quite enough.