I tried Zerene and Helicon, each left ghosting. And yes this was for macro work of flowers, mostly creative work. At micro levels, you have to be discerning about what to include in or out of focus.
Maybe therein lies the problem, just missing the required shots for a smoother transition. The usual issue is with occluding features. When focusing on features further away, foreground features become somewhat transparent and the blending has trouble deciding which sharp image to use, foreground or background. HeliconFocus' Method B (using a depth map) is better at getting the edges right, because Method A uses averaging which is better for surface structures. The recently added Method C (pyramid) may also work well. It can work well if you combine parts of the the A/B/C output by using the retouching functionality of HF Pro. Zerene also offers retouching capability if I remember correctly.
It's a different proposition for landscapes. You mostly want everything in focus. What I did not try was combining large numbers of images. I used only 5 or 6 at most.
Depending on the magnification factor, that may be too few. Based on the magnification factor, you can use the (slightly less accurate, but accurate enough) DOF approximation formula for close-up and macro photography
, which uses the magnification factor as input. Your sensor size in relation to the size of your object will give you the correct magnification factor to use. The CoC to use in that formula equals the sensel pitch, if you want seamless sharpness per pixel from front to back. If you are going to output at less than pixel per pixel size, you can increase the CoC proportionally.