'Shared history' means the history that the countries share. That could be good things such as trade, sport, and shared culture, or bad things such as wars and retaliations. Basically - things that the countries have done together. Here, it is 'shared history as ... allies'.
There is no 'is', so neither of your sentences is correct.
You can perhaps read [countryA-countryB] shared history more clearly as 'history shared between countryA and countryB'.
So - the basic sentence is "he says it marked a milestone", or expanding "he states how it marked a milestone in their history as allies", and if you expand that, you get the original sentence.
Does that make more sense?