AFAIK that is how the existing attempts to match Linear A to a language worked too. But perhaps the machine could do it better.
I will say that as a teenager, mass lexical comparison, in Merrit Ruhlen's book 'The Origin of Language: Tracing the Evolution of the Mother Tongue', was very compelling. Ruhlen worked closely with Greenberg, who was a famous historical/comparative linguist of African languages.
Ten or more years later, with the benefit of experience, I feel like aligning hundreds of languages in a common vector space (multilingual word embeddings) will probably answer these questions better. But I am not a comparative linguist.