No, it's not "whatever his reasons were for, wanting" but "whatever his reasons were for (wanting)". He has reasons for something. The whole "for" phrase could be replace by a dependent clause: whatever his reasons were, which made him want it to be that way.

In Russian maybe something like несмотря на то, какие у него причины, чтобы хочеть, что вещи так будут. Or something like that, which may not be the way you'd actually put it.