Cooking through thick liquids
This answer presumes your worry is that by not putting in the pulses/tubers from the beginning, you're actually not ending up with the "correct" result.

My experience with recipes (even from reputable sources) with regard to slow cooked, stewy dishes, with ingredients that take time before they're done, is that they're either short on time, or short on liquids. Either that, or I'm bad with measuring, use ingredients of lesser quality, or suck at cooking (most of the time I suspect the latter two are the guilty parties).

But most likely (and here's the good part), the pulses/tubers are there from the beginning to act not only as a nutritional component, but also serve a dual function as thickener. They're most definitely (IMHO) not there from the beginning to impart flavor to the curry.

So one of the solutions you've already found yourself: 
Cook the pulses/tubers separately, and add them in the end. The curry will not suffer any loss in flavor. If it's to thin, either squish some of pulses so the starches can thicken it, or reduce a bit longer.

Second solution: Start out with more liquid than the recipe prescribes, and cook/reduce longer, until the desired thickness has been achieved.