It does make sense in context, but I’d drop the “so” in English. The commas delineate a subordinate clause, i.e. subject and verb that support the main sentence.
“The existence of the EU, it seems, barely 20 years after it’s creation stands on the brink…”
German is stricter about maintaining references between clauses than English is. That’s one of the reasons the so-called “da Wörter” are used a lot in German whereas their counterparts in English hardly ever get used despite serving an identical grammatical function. In this case, the “so” refers to the condition stated in the main clause. In English, including the “so” makes it feel like it should come at the end usually joined with an “or.” “The existence of the EU stands on the brink barely 20 years after its creation, or so it seems.” It conveys tone rather than substance, so it can and should be left out of your own writing if you don’t have a solid intuitive feel for the way it colors the tone of the statement.