Is it necessary to only boil vegetables (or chicken) or can they be pressure cooked and later be boiled for the flavour to seep in?
This recipe confuses me in a number of ways.
First the simplest: It calls for adding the remaining spice powders in two places, steps 5 and 7.
One of my favorite food ethnicities is Indian, and in all my years of cooking and eating it there has always (with very rare exception) been one very important rule:  Cook the spices. The difference in both taste and texture is what really what makes the food.

In my opinion, this is what you should be doing:  In a small skillet heat a couple of tablespoons of oil until the oil is shimmering, the add the cumin seeds and fry until they become aromatic.  Add the remaining spices; coriander powder, turmeric powder, chili powder and the gharam masala and cook about 2 minutes, stirring constantly.  Set this pan aside.  In your cooking vessel, fry the onion and the chopped green chili until softened, then add the ginger-garlic paste, sauté just until aromatic, then add the tomato and the pan of cooked spices.

As far as your first question regarding boiling or pressure cooking the vegetables, not sure I understand why you would want to.  Have you thought about cooking everything in the pressure cooker, including the chicken?  If that sounds appealing then use the above method for the spices, onions and green chili, then add the veggies, water and, if using, the chicken (par-cooking the chicken can save time).  This is the method I use when using a slow-cooker which should work for this.

As to question 3, go ahead and add salt at the beginning when adding the veggies, and the add more to taste after the major cooking.  And yes to both of the final parts regarding the salt and the "greasy" layer (prefer the word "oily").  Adding salt early in the cooking process can make a lot of difference in both taste and texture, and the oily layer (which comes from the frying of the spices) carries a lot of flavor.

I hope this helps.  Ask more if needed.