Toss apples, pumpkin and lemon juice in a large casserole dish, cover and bake for 2-2 ½ hours, until very soft.
Allow to cool slightly, then add apples, pumpkin and any liquid to a food processor and puree completely, making sure peels are finely ground. Alternatively, use a food mill to remove the peels and seeds.
Scrape back into the casserole dish, re-cover and bake another 1 ½ hours, stirring halfway through.
Remove the lid and bake a further 30-40 minutes, stirring every 15-20 minutes, until very thick.
Cool to room temperature (or cover and chill until needed – up to 1 week).
When ready to use, add cinnamon, sugar, cornstarch, tapioca starch and egg yolk, mixing well with a spatula. Set aside while preparing pastry.
Cream the cream cheese, shortening, and sugar until fluffy.
Add vanilla and beat at medium speed until well blended.
Beat in flours, flax seed, baking powder, salt, nutmeg and cinnamon until well blended, adding milk as necessary to for a stiff but cohesive dough.
Shape into a disc and wrap tightly in plastic. Chill at least 2 hours, until firm.
Preheat the oven to 400°.
Between sheets of waxed paper, roll the dough into an approximately 15” round.
Flip into a greased 11” tart pan with a removable bottom set on a baking sheet, pressing into the sides. Trim the edges.
Dock dough with a fork, then line the shell with foil and fill with pie weights or dried beans.
Bake for 25 minutes, then remove the weights and foil and bake for about 5 minutes, or until the base of the shell is golden.
Transfer to a rack and cool 30 minutes. Leave oven on.
Spread the apple-pumpkin mixture into the tart shell.
Starting at the outside, overlap the apple slices in concentric circles over the pumpkin filling. Sprinkle with the raw sugar.
Bake for about 1 hour, or until the apples are tender and golden and the custard is set in the centre.