Related languages are different due to changes; but they haven't all changed in the same way. Thus it is perfectly sound to describe one language as closest to the common substrate of other related languages.

Here's an abstract example.

    L1: abcxfgziqk
    L2: qbcdvgxijk
    L3: awcdughrjk
    L4: abcdzghijk

Looking only at languages L1 through L3 we may infer a common ancestor from what is more shared. Saying that L4 is closest to this hypothetical language is not an empty concept, or artificial based on some ideology.