Trying to 'fill' it won't help other than filling the void with something.
You see the problem is that you have already applied glue to the woods there and therefore the pores are already filled glue and are unable to accept any more for a decent bond.
Remove the backing and redress the surfaces. Remember that area is under more strain than anywhere else and a failure there is likely to be spectacular! The other point is that the area mustn't have had sufficent clamping pressure and you don't know what is going on with the glueline where you can't see/next to the gaps. It isn't worth leaving it for it to break down the line.