Whichever conjunction comes after if only doesn't really matter. Since you haven't provided a specific example sentence, I can only give you a general answer. It (hypothetically) stands for (even) if [that is so] only as... or, more informally, (even) though [that is so] only as... I believe the latter sense is most prevalent, although though only as would be more precise in that case. A few example sentences:
I don't know whether he is infatuated with Socrates, but Crito will help the great thinker, if only as a fellow philosopher.
Crito will help Socrates, (even) if he does so only in his capacity of a fellow philosopher.
The Roman Empire remained after the fall of Romulus Augustulus, if only as cultural entity.
It is a matter of controversy whether the Empire continued as a political entity after the fall of the last Roman Empire, i.e. there was some sort of empire under the Goths, and the Byzantine Empire could be said to have inherited its essence; but, no matter what, we say it was still there, even if it remained only as a cultural entity.
Nero and Agrippina get along quite well, if only as partners in crime.
They get along well, even though they only get along as partners in crime, not in other capacities, such as mother and son.