I recently tried Nigella's Crustless Pizza from Kitchen. I doubled the recipe, used half whole wheat flour, half all purpose, and split between two aluminium pie plates. The dough came out quite dense and wasn't cooked through even after nearly an hour in the oven at 400 F (200 C). The crust was also nearly 1cm thick. Do you have any suggestions other than using less of the batter. I also found that the pizza stuck to the dish a bit so I will grease the pan more liberally next time. Thank you.
Nigella's Crustless Pizza (from Kitchen) has a base that is very similar to a Yorkshire pudding (popover). As the base contains a relatively high proportion of egg and liquid to flour it will rise up as it bakes and so will be thicker than a yeasted dough base and will also not be as crisp as a thin dough base.
If you doubled the recipe and then split the batter between two 8 or 9 inch pie plates then you should not have a problem with there being too much batter. Unfortunately using part whole wheat (wholemeal) flour will mean that the crust will be denser and slightly more chewy due to the bran in the flour and also as whole wheat flour tends to absorb slightly more liquid than all-purpose (plain) flour. The cheese in the batter will mean that the centre remains a little soft, even when fully cooked, and we suspect that you experienced this rather than an under-cooked base. However you should make sure that you cook the dish on the centre shelf or above in your oven and you may also find that it helps to use vegetable oil for greasing the pan and also preheating the pan in the oven before adding the batter. If the pan is hot when the batter is added then it will help to give the batter an initial boost and should help the centre to cook quickly.