Post Update: still if you read ISRG's statement carefully they went to grate lengths not to accuse Comodo of Illegitimately acquiring trademarks, but instead to defend their preexisting claim to the use of the "Let's Encrypt" trademark; which in the USPTO's own words "differs from the right to register." [p. 12, http://www.uspto.gov/sites/default/files/BasicFacts.pdf]
Moreover what Alden claims by saying that they were just going to let the claim's time run out and forgot to notify ISRG is just as crafty, because you only get to keep the claim to the use of a trademark if you're willing to defend it and by just letting the clock run down it could be argued that Comodo's use went uncontested. Yet Aas's rebuttal that they wont consider the matter closed till Comodo withdraws seems to have that covered at least in spirit.
I guess in the end it may come down to how true in letter and spirit the this statement by USPTO is: "In the United States, parties are not required to register their marks to obtain protectable rights. You can establish “common law” rights in a mark based solely on use of the mark in commerce, without a registration." [p. 10-11]