It's only worth the other (albeit often minor) penalties for toe-in to improve the thrust asymmetry for VMC if you are going to be VMC-limited for performance and if the fin size is driven by VMC.
If VMC isn't going to be a performance constraint, it's unlikely I'll care enough to drive the engine layout by it. Instead I'll be looking for the most aerodynamically efficient layout, considering both thrust and drag issues.
If VMC is important, but something else is driving the fin size more - such as high speed directional stability, say - then I can take advantage of the large fin that the other requirement drives, and I get it "for free" for VMC. That means I probably won't need to worry about toe-in for that case either.
As always, the best design is a compromise, and the weighting factors on that compromise can be different, which can subtly (or radically) affect the design decisions. Which is why there's rarely a single right answer to a design question. (Though there are also lots of bad answers!)