This is a reduced relative clause, not a special construction with so. And the comma's necessary.
- ... physical activity, so vital for the developing body, is often overlooked ...
is shortened by ordinary Whiz-Deletion from
- ... physical activity, which is so vital for the developing body, is often overlooked ...
Since this is a parenthetical (nonrestrictive, supplementary) relative clause -- the kind that has to use which, and is ungrammatical with that -- the comma is necessary in order to indicate the intonation contour that distinguishes it from descriptive (restrictive, integrated) relative clauses in speech.
On the other hand, many would deprecate the use of so as an intensifier here; it marks the sentence as somewhat florid, reminiscent of advertising. In other words, it sounds like handwaving, done to avoid saying exactly how vital exercise is, thus presenting a claim without evidence for it.