I'm not entirely sure what you mean by this (I haven't read the article yet, and I'm already familiar with Loeb's theorem). It's true that you cannot show that, say, second order arithmetic is consistent in the same system. In fact, every soundness proof (for a sufficiently strong logic) will have to be carried out in a stronger system.
There is a standard way around this, which has existed for a long time. You stratify the system by introducing universes. E.g. in type theory, a universe is a type of (codes for) small types. This allows you to state and show meta theorems "for all (small) types", by quantifying over a universe.
In the concrete example of Martin-Loef type theory (MLTT) you can show that MLTT with n+1 universes contains a model of MLTT with n universes. On the other hand, adding more universes seems to be harmless as far as anyone knows.
Under the assumption that MLTT with a countably infinite number of universes is consistent and you restrict your formal system to only use a bounded number of universes, it is still possible to show that it is "reliable". It is "at least as reliable" as MLTT with countably many universes.
I will read the article later and update this post if there is something compelling in the paper. At the moment I'm just confused what the problem is, and would really appreciate it if you could expand on this.