This came up as an issue at my old employer. QC decided we were wrong by showing the funding fee on 902. My opinion was (and was ultimately backed up by several sources) was that the VA Funding fee is the same at FHA UFMIP or any other conventional One time MI payment and as such should be in the 900's as TR noted.
My interpretation of the reference on page 49 of the FAQ's were agency related fees such as the FHA Commitment fee, etc. We did not interpret that to mean the funding fee. FWIW, the VA told me they didn't really care which line it was on (although it isn't under thier authority), and it was never brought up as an issue by our investors.
Worst to first back to worst