There is no reason to believe the symbolic encoding would be the same. For example, if they evolved with 8 fingers instead of 10 they could be driven to encode their symbols in a base 8 system.
I think the point of the OP sharing the PBS spacetime video in this context is that we have reason to believe that the fine structure constant is truly constant throughout the universe. So if the aliens have the capability of measuring and reasoning about electron orbitals and their binding properties with nucleus, then there will likely be significant overlap between our mutual concepts of 'fine-structured-constantness'. Just made that word up. :-)
This would be independent of encoding scheme and independent of practical communication issues.