The decision-theoretic argument is not supposed to prove everything. It's supposed to explain why agents living in environments that have so far been stable should set their credences according to the Born probabilities. So, yes, there are presuppositions involved. But I don't see how this is a devastating problem for Everettianism.

You brought up Boltzmann brains. It turns out that our best cosmological models predict that most observers in the universe will be Boltzmann brains. The universe will gradually approach an eternally expanding cold de Sitter phase, and thermal fluctuations in quantum fields will produce an infinity of Boltzmann brain type observers. Do you think this is a devastating objection to cosmology? I think the appropriate tack is to recognize anthropics as an important issue that we need to work on understanding, but in the meantime proceed with using those cosmological models under the assumption that we are not Boltzmann brain type observers.

Anyway, the kind of problem you're raising now is not one that Wallace's decision-theoretic argument is intended to solve. This paper by Greaves and Myrvold might be relevant to your concerns, but I haven't read it yet: http://philsci-archive.pitt.edu/4222/1/everett_and_evidence_21aug08.pdf

The abstract:

Much of the evidence for quantum mechanics is statistical in nature. Relative frequency data summarizing the results of repeated experiments is compared to probabilities calculated from the theory; close agreement between the observed relative frequencies and calculated probabilities is taken as evidence in favour of the theory. The Everett interpretation, if it is to be a candidate for serious consideration, must be capable of doing justice to this sort of reasoning. Since, on the Everett interpretation, all outcomes with nonzero amplitude are actualized on dierent branches, it is not obvious that sense can be made of ascribing probabilities to outcomes of experiments, and this poses a prima facie problem for statistical inference. It is incumbent on the Everettian either to make sense of ascribing probabilities to outcomes of experiments in the Everett interpretation, or to find a substitute on which the usual statistical analysis of experimental results continues to count as evidence for quantum mechanics, and, since it is the very evidence for quantum mechanics that is at stake, this must be done in a way that does not presuppose the correctness of Everettian quantum mechanics. This requires an account of theory conrmation that applies to branching-universe theories but does not presuppose the correctness of any such theory. In this paper, we supply and defend such an account. The account has the consequence that statistical evidence can confirm a branching-universe theory such as Everettian quantum mechanics in the same way in which it can confirm a non-branching probabilistic theory.