The quoted sentence is:
And finally, we need to take this very seriously, if not for other reasons than because in the end it is not only up to the researcher to define what is critical or fruitful.
Isolating the key parts of the sentence (with some paraphrasing) gives:
we need to take this very seriously
because [ultimately] it is [up to all of us — not only the researcher]
to define what is critical or fruitful.
if not for other reasons than ...
implies that there might be other reasons for taking it seriously, but
here's the over-riding reason:
I agree that the wording of the sentence is inordinately and unnecessarily complex!
As regards your more generic question about three possible constructions, I'm assuming that the periods/full-stops at the end of each example are intended to indicate the end of a sentence, and I've construed them accordingly.
I cannot think of a construction where "[claim/statement], if not for reason." would make sense.
You could have a statement of the form:
We should do XYZ for [reason A], if not for other reasons.
That would suggest that 'reason A' is an over-riding reason, even though there may also be additional reasons for doing XYZ.
A statement of the form
We should do XYZ, if not for other reasons than because [reason A]
is effectively the same as item 2. above expressed the other way round. It may be possible to have a similar statement without the word "because", but I can't currently think of one.