First it uses the current average temperature of the universe. Lowering the temperature can be done by just waiting a while before turning the machine on. I assume that powering a sufficiently powerful fridge is not an option, given the origin of the theoretical limit, but I can't quite point out why it wouldn't work.
Secondly it assumes that an unsuccessful attempt must flip at least some bits in an semi-permanent manner. This is obviously true of all current computers, but doesn't have to be true for all possible apparatuses. A specialized hyper-efficient password cracking system should be expected to get below this limit. Will we ever build one? Who knows.
Arguably this latter 'loop-hole' is just pointing out that quantum computers or more efficient algorithms could do better, so maybe we should absorb it into the definition of 'brute-force'.