I think it might be helpful to have both paragraphs:
Similarly, when we talk about arithmetical statements being true but undecidable in PA, there is no need to assume that we are introducing any problematic philosophical notions. That the twin prime conjecture may be true although undecidable in PA simply means that it may be the case that there are infinitely many primes $p$ such that $p + 2$ is also a prime, even though this is undecidable in PA. To say that there are true statements of the form “the Diophantine equation $D(x_1, \ldots, x_n) = 0$ has no solution” that are undecidable in PA is to make a purely mathematical statement, not to introduce any philosophically problematic ideas about mathematical truth.
Similar remarks apply to the observations made earlier regarding consistent systems and their solutions of problems. It was emphasized that the mere fact of a consistent system S proving, for example, that there are infinitely many twin primes by no means implies that the twin prime hypothesis is true. Here again it is often thought that such an observation involves dubious metaphysical ideas. But no metaphysics is involved, only ordinary mathematics. We know that there are consistent theories extending PA that prove false mathematical statements—we know this because this fact is itself a mathematical theorem—and so we have no mathematical basis for concluding that the twin prime conjecture is true, which is to say,that there are infinitely many twin primes, from the two premises “PA is consistent” and “PA proves the twin prime hypothesis.”
From the earlier paragraphs in the section, it seems that 'mathematical truth' is essentially truth in $\mathbb{N}$ (or $\mathbb{R}$, or whatever natural universe we're working in). I believe the point here is that PA is not complete, so there are (or, at least, there could be) consistent extensions S of PA which could prove both that PA is consistent and that the twin prime hypothesis is true. But that these extensions could also state, for instance, that some other theorem of $\mathbb{N}$ is false. So the statements 'PA is consistent' and 'PA proves the twin prime hypothesis' formally imply that the twin prime hypothesis is true, but care should be taken as to what consistent system this is being proved in (in particular, what system is proving that PA proves the twin prime hypothesis).
But there's nothing wrong with your reasoning. If $PA \vdash \phi$, then of course $\mathbb{N} \vDash \phi$.