I agree it seems utterly absurd, but they've seen every single junior coalition partner of theirs lose seats by virtue of being the junior coalition partner and now they are in that position they probably want to avoid it and play the classic post-modern political trump card (very popular amongst their liberal brothers down south) of both governing and acting as if they are fresh opposition. It's the only explanation I can think of.
This + fears of NSC staying outside this government and taking their votes plus those of the PVV if things go wrong. Looks like a game of who blinks first, but the VVD have more to lose by not entering (disappointed voters who voted for them because they 'offer stability') and potentially more to win by entering (many PVV voters could flow more easily to the VVD). In any case, if the VVD are banking on a failed formation and a new election, they are playing a very dangerous game. Yesilg�z' image is in the gutter now - and purely based on the election result it didn't have to be that way.
VVD knows that jumping straight into bed with Wilders would tank daddy Rutte's bid for NATO leadership.