I never pay any attention to the dots unless the lighting conditions are so bad that I can only see the dots..And does that mean that the alignment of the three dots will be off?
Here's why:
1. Dots aren't always aligned when the sights are aligned,
2. Not all sights have dots.
3. Precision sight alignment using dots only isn't really possible.
I see dots like "night sights lite". They help with rough sight alignment, especially in poor conditions, but are of no use otherwise.