The question is, if it is only a change in PCB layout, what was the reason for the change in the PCB layout?
If a for profit organization expends funds to make a change, there has to be a reason. This is particularly true if in making that change, you add a revision number to make it easily identifiable to support which board the customer is calling about. The fact that in this case they not only called it a revision, but labeled it a new version only emphasizes the importance of the change. I do not think they would call it a new version simply because they moved a component a few millimeters or rerouted a trace.
Lastly, I would not expect the specs to change. They are not coming out with a new board, only making changes to an existing board, perhaps because the original board did not meet all the specs, or had some short coming that created a lot of support issues.
Simply put, I think it could easily matter, and I would like to know what the differences are before making a purchase where the vendor does not specify which board they are offering.