Validation of computer modeling simply cannot be done unless the models move from the computer into the "real world" so that the models can be validated. That simply has never happened in the use of modeling to study evolutionary processes.
You appear not to understand how ancestral phylogenetic trees are reconstructed. This is not a computer 'model', in the sense, say, of a climate model. It's a mathematical process that reconstructs the most likely common ancestor. It can be reproduced by anyone else who knows how to do such analysis.