Yes, but it is not sent to WinBoard.
What do you mean by that? The only time the options are sent to winboard is after the protover 2 command. I used your config file and it worked correctly.
[Polyglot]
EngineCommand = toga2
LogFile = foo.log
[Engine]
NullMove Pruning = Never
This is the answer to the xboard/protover 2 command.
feature done=0
feature analyze=1
feature colors=0
feature draw=1
feature ics=1
feature myname="Toga II 1.4.1SE"
feature name=1
feature pause=0
feature ping=1
feature playother=1
feature reuse=1
feature san=0
feature setboard=1
feature sigint=0
feature sigterm=0
feature time=1
feature usermove=1
feature memory=1
feature smp=1
feature egt=""
feature variants="normal"
feature option="Search Time -spin 0 0 3600"
feature option="Search Depth -spin 0 0 20"
feature option="OwnBook -check 1"
feature option="BookFile -string performance.bin"
feature option="Bitbases Path -string c:/egbb/"
feature option="Bitbases Cache Size -spin 16 16 1024"
feature option="MultiPV -spin 1 1 10"
feature option="NullMove Pruning -combo Always /// Fail High /// *Never" <------------------------
feature option="NullMove Reduction -spin 3 1 4"
feature option="Verification Search -combo *Always /// Endgame /// Never"
feature option="Verification Reduction -spin 5 1 6"
feature option="History Pruning -check 1"
feature option="History Threshold -spin 70 0 100"
feature option="Futility Pruning -check 1"
feature option="Futility Margin -spin 100 0 500"
feature option="Extended Futility Margin -spin 200 0 900"
feature option="Delta Pruning -check 1"
feature option="Delta Margin -spin 50 0 500"
feature option="Quiescence Check Plies -spin 1 0 2"
feature option="Material -spin 100 0 400"
feature option="Piece Activity -spin 100 0 400"
feature option="Piece Square Activity -spin 100 0 400"
feature option="King Safety -spin 100 0 400"
feature option="Pawn Structure -spin 100 0 400"
feature option="Passed Pawns -spin 100 0 400"
feature option="Toga Lazy Eval -check 1"
feature option="Toga Lazy Eval Margin -spin 200 0 900"
feature option="Toga King Safety -check 0"
feature option="Toga King Safety Margin -spin 1700 500 3000"
feature option="Toga Extended History Pruning -check 0"
.... snip ....