Etymologists have encountered similar linguistic features in

Etymologists have encountered similar linguistic features in widely varying language groups, which are consistent with the theory that all languages can be traced back to a common root language.

(A)which are consistent with the theory that all languages
Incorrect: "which" modifies the noun right before the comma "language groups". Now, you're saying that "language groups are consistent with the theory ...". This doesn't make logical sense.
(B)where the theory that all languages are consistent
Incorrect: "where". "Where" can only be used in reference to physical places. Ex: "In France, where ..."
(C)consistent with its theory that all languages
Incorrect: #1) What is "consistent with its theory"? We can't answer this question given the previous clause. #2) "its" does not have an antecedent. What does it refer to?
(D)findings consistent with the theory that all languages
CORRECT: "findinigs consistent with the theory ...." modifies the whole previous clause. This information only adds additional information to the previous clause.
(E)findings that are consistent with the theory that proposes that all languages
Incorrect: Gramatically correct but way too wordy compared to choice D.