It all reminds me of the perfect is the enemy of good arguments.
Is soylent perfect? Most likely not, is it better then the vast majority of people are eating? that wouldn't be a high bar to jump, and I think it jumps it easily.
Even when trying to lose wieght, making sure you hit your minimum protein requirements is important... my only suggestion to someone taking a reduced amount of soylent is that they really should supplement extra protein into their diet. Especially if exercising as they are likely losing a lot of muscle with the fat loss, which is probably not the desired result.
Saturated fat sensitivity seems to have been my issue (VERY difficult to be on that diet without high levels of saturated fat) and I'm now on a low-carb monounsaturated fat diet that has dramatically improved my blood lipids.
So, for me at least, I would have to disagree with "the rest is just calories" statement. I think too many people are trying to simplify nutrition with a single book, diet, or pill, when in reality, it's a complex system that might very well be impossible to predict.