The action of GR is proportional to the Einstein-Hilbert action $$S_1=\int \sqrt{-g}R dx^4.$$ Now, $R$, contains terms of the form $\partial^2 g$. Using integration by parts, one can write this entirely in terms of first derivatives $\partial g$. The two actions are equivalent except for boundary terms. Lets call the action with only first derivatives, $S_2$.
Now, if the action of $S_2$ had been discovered first we might consider it the action for GR.
If these actions are inequivalent due taking boundary terms into account, how do we know which is the "true" action for our Universe? This surely means there are two inequivalent theories which may disagree cosmologically.
Indeed the action $S_2$ may be more useful when considering quantum gravity.
When I read papers and they talk about the boundary terms of GR I usually skim over it as seemingly irrelevant. But I assume it is not irrelevant otherwise they wouldn't have mentioned it in the first place.
If the boundary terms are satisfied for our Universe it means that $S_1=S_2$. But if not does it mean they are different theories of gravity? And if so, how do we know which one is correct?