It is difficult to give an authoritative answer because who knows what a "typical" pie might be like. It might be different for every person you talk to. I will therefore answer just for myself.
All of the made-from-scratch pudding pies that I have made have been very similar- a lot of sugar and fat and some starch to make the gel. Usually recipes also call for egg yolks which also help with binding but make the pudding a little more custardy instead of just a gel.
The texture should be sliceable so that the sliced edges sag but don't flow. I have had pies that have to be scooped out which, while perfectly delicious, isn't as nice a presentation. On the other side of the spectrum is what you have- rubber- which is a great presentation when cutting but not much fun to eat.
Gradually adding your corn starch slurry is always a good idea. Often the starch is mixed with the sugar to make sure it is evenly dispersed and then added to the liquid. As long as you didn't have clumps your technique here was fine.
I don't think your expectations of a banana pudding pie or your technique are wrong. What I think is slightly wrong is your expectations for this recipe. It's "wrong" to call something a "take on a southern classic" that uses soy milk and organic margarine. The milk fat and egg yolks in typical recipes do a lot to make a smooth, custardy pudding. Doing this with different fats and soy milk could be good but I would expect it to be different.
The bananas don't have to be precooked- that would be horrible, I haven't used earth balance but if it behaves like normal margarine then your crust sounds like it is pretty normal. The number of bananas also sounds reasonable. You want a good layer but not so much that the pudding can't work in to bind it together.
Reducing the amount of corn starch a little should make the filling softer and more to your liking. You could try adding a little more fat which will also soften the pie. In the end though, I wouldn't expect a typical texture of a pie that is made completely of non-typical ingredients.
Jeni's Splendid Ice Creams at Home by Jeni Britton Bauer has a (somewhat) similar base to this, in that it has no eggs, and uses a mix of milk and cream - along with a tiny bit of cream cheese to provide the requisite proteins, and corn starch to thicken.
In my opinion, it's one of the best ice cream bases out there.
I also have the Perfect Scoop, and have had no trouble switching the recipes I've tried from it over to Jeni's base.
Best Answer
I would argue that it is the gentler methods like Doug suggested which create problems. They are intended for eggs only custards, not eggs-and-starch. If you use them, you risk that your mixture doesn't get hot enough. Then your starch stays uncooked, and your eggs' starch-digesting enzymes stay intact and can liquefy everything.
If you use either starch only, or a mixture of eggs and starch, your custard has to boil. I slurry the starch with a bit of the milk, never tried it with the eggs. Then add the slurry to the almost-simmering milk (which already contains sugar and flavors), and pour in the tempered eggs afterwards if using them. From the time the starch hits the liquid, you have to stir constantly or you risk burnt bottom, so you don't want to do it too early, but if you do it too late, the stream of slurry will start gelatinizing before it has been dispersed in the milk, and will clump. So, do it just before simmering, or if it has started to simmer, take it off the heat, mix it there, then back on the heat.
After you have the slurry well mixed in, you simply stir slowly until after it has blubbed. You will notice a moment when it goes from liquid to thick, this is when the starch starts gelatinizing. Less than a minute later you should see the boil bubbles, which are very large and slow-forming in the viscous liquid. That's the time to take it off the heat, your starch is fully cooked and will not taste chalky. If you are serving it for a fussy occasion, it makes sense to pass it through a sieve to catch stray clumps of starch or egg protein, but I usually don't bother.
If you were trying to keep the eggs from overcooking, that's impossible. Eggs overcook at around 87 C, while starch gelatinizes around 96 C. Also, the yolks will eat up your starch after 24 to 48 hours if not heated well. So you cannot keep the taste of a starchless custard if you use starch. That's not a problem texture-wise, since the starch takes care of the texture and you don't get the corning or whey exudate associated with overcooked egg custards.