I also have to use the micro adjusts in order to get perfectly matching angles. Usually the two sides are only slightly off from one another (0.2 degrees or so). As long as you can get them to match using the micro adjustments, I don’t see a reason to be concerned. From a use perspective, I don’t think you would be able to feel much of a difference between a knife with perfectly symmetrical 20 degree bevels and an unsymmetrical 23 / 20 beveled knife let alone one with 20.5 / 20 degree bevels. That said, the reason anyone buys a Wicked Edge product is because they want this level of control over the sharpening process.
I recall reading in an old thread that Wicked Edge does measure the amount of difference in the angles when they are doing quality control on the generation 3 sharpeners and there are limits to what they deem to be acceptable (I don’t recall the numbers, but you might try searching the forum to find the values). You can give them a call and ask about it if you think that yours might be out of specification. The Wicked Edge team has superb customer service and I think they’d be happy to talk to you about it.