These are very different products and so it is no surprise that the effects
of heating on the nutritional value might be different.
AFAIK, tofu is perfectly fine to cook but, yes, miso should be added nearer
the end (although I usually don't do it that way - just slack, I guess).
The difference is that miso is a fermented product and tofu isn't - it is
made by grinding soybeans with water to a milk, straining it, and setting it
using nigari, epsom salts, or similar. Basically, cooking tofu is little
different (I would think) to cooking soybeans - except that it is much