yes, all the Zbrush tools are dependent upon topology in some way. Except for maybe projection master which works with UV projections. I recommend using dynamesh with retopo tools for less distortion in your maps, but doing it the old way can be alright.
One other thing to mention is the size of your texture maps. 2048 x 2048 is not really large enough for a mesh of 3 million polys. If a map of that size had UVs that used all of its space it could only support 4 million polys. In practice UVs never use 100% and yours something like 50%, meaning that you’ll be losing detail.