Well the point isn't to have a form of PIE that is completely accurate. The point is to use it as a neutral, naturalistic language that can create a common identity - and you really can't get more common than the common ancestor of most European languages. Modern Hebrew is very different from the Ancient Hebrew that it imitated while it was revived - an easy example is in how the ancient and modern phonologies differ - and if the language changes once it is revived, that's fine. The point is to get one close enough. If you read the grammar outline that I posted you can see that it's extremely trivial to create words and concepts that did not exist in PIE through back-deriving words into their MIE constituents.
Hell MIE doesn't even attempt to be an exact model of PIE - it's an imitating of a specific dialect and uses new constructions that would be helpful for modern european speakers, such as the creation of separate past and future tenses; PIE did not have temporal tenses; the "tenses" were primarily aspectual.