at what temperature should apple-choco pie be prepared?

The pre-baking of the pastry is missing a "how to tell when it's done" instruction. My guess is there's a good chance you didn't bake it long enough. In general, when pre-baking plain pie crusts, you're aiming for golden brown. It's a bit harder to tell when it's got the brown from the chocolate in it, but if you look closely you should still be able to see the change in color. It should also just look cooked - a bit of texture develops on the surface and it appears to have dried out. As SAJ14SAJ suggests, you also normally pre-bake crusts with weights in them to keep them from bubbling too much. (This is also why you poke holes.) A common method is to cover with a piece of foil, then fill with dry beans.

As for temperature, in my experience, pie crusts are generally pre-baked at 350°F. But the important thing is to check and know when it's done.

Now, baking the filled pie. This is the weird thing - usually apple pies don't use pre-baked crusts, because it takes more like an hour to fully cook the apples til they're soft. Maybe you didn't like the apples because they were still crunchy and a bit raw, and the flavor hadn't smoothed out with the nuts and sugar? If that's the case, you may want to skip pre-baking the crust, and instead fill and cover the pie and bake it all together, for 45 minutes to an hour. If the crust browns too much, you can loosely cover it with foil.

If on the other hand, you like the apples like that, or the quantity of apples is sufficiently small that they're actually cooking fully, then sure, stick to the recipe. (You could increase the temperature to 350°F here too, but that'll mean the crust is done when the apples are even less done.) If you've properly pre-baked the crust, you shouldn't have problems with the bottom of the pie being undercooked.

We can only guess at the cause of your quality problems with the bottom crust.

If it is due to excess moisture from the filling seeping into the crust, there are two main approaches you might take.

1. Par-heat the apples (as recommended by Kenji Alt) after they are cut up, but prior to baking. This will help set the pectin and cause them to loose less moisture into the pie as it is baked. You can do this in the microwave, or by pouring hot water over them. See the link for details.

2. Create a barrier layer between the bottom crust and the filling with a complimentary ingredient moisture will not (quickly) penetrate.

Protecting bottom crust with a barrier

I would suggest using a thin layer of semi-sweet or bitter-sweet chocolate. Complimentary thick preserves, such as apple or peach may also work:

1. Blind-bake the crust as directed (bake it without a filling). Edit: It is strange that your recipe does not say to dock the crust before blind baking, nor to use pie weights, or rice, or something to keep it from bubbling up and buckling.
2. Spread melted chocolate (or preserves) in the shell.
3. Pour the filling on top, being careful not to disturb the barrier layer too much.
4. Bake as normal.

Quality of Recipe

The recipe has a number of strange aspects, as Jefromi and I have both noted in our answers such as a low temperature, time/temperature ratio for the apples, not specifying type of apples, in addition to poor blind baking instructions.

You might be better off searching for a better quality recipe that tickles your fancy.