Do you have any pointers for this? I also use Helicon with the Alpa and in my experience it takes a lot more shots to get the equivalent DoF that I get from my 35mm full frame gear. I now over compensate with close up foregrounds after shooting lots of scenes with disappointing close up critical focus. This isn't an Alpa only issue btw - same thing for me with my Phase One DSLR with pretty much anything other than a 28 or 35mm.
I had the same difficulty you are describing and it is extremely frustrating.
A few suggestions based on my experiences:
First be sure your lens is calibrated to infinity with your body and back. Two of my four lens were off and it made a huge (read HUGE) difference. The tolerances are extremely small and my lens that was calibrated past infinity was a stinker. Once calibrated they are scary sharp.
Test your equipment so you know the exact distance where critical focus is at for each lens at all usable apertures and focus settings.
What I did was focus the lens to infinity and take a tethered exposure at each aperture. The subject should be something that is easy to measure the distance from the camera to the closest spot with critical focus. Since I print my images large I want them to appear sharp at 100%, if you print smaller such as 16x20 "apparent" focus can be determined at 25%-50% display.
I do the same at each aperture setting on the helical focus ring out to two stops shy of the aperture. For example, at f/16 I will test and record the nearest focus at f/5.6 and f/8. You will notice that the sharpest image will be at infinity with the overall sharpness degrading the farther you focus from infinity until it is obviously front focused (more than two stops shy of the aperture in my estimation).
I created a chart for each lens with the apertures, focus settings and closest distance it was in focus. For example: on my 35xl, f/11 focused to f/5.6 everything from 4' or so to infinity is in focus.
While shooting I use the sharpest setting that will keep my image in focus. If the subject to infinity can be kept in focus with the lens focused on infinity at f/8 I'm using the sharpest setting available. If the foreground is too close I'll either stop down or dial in some front focus as long as I am within two stops of the aperture.
In this way, I know my subject is in focus and I'm using my equipment in the most efficient way possible. In my tests with the p65 and 72L I can stop down to f/16 at infinity with almost no loss of sharpness that can't be easily corrected in post. At f/22 and f/32 I can get acceptable sharpness at infinity but any front focusing closer than infinity and all bets are off.
I initially used a laser distance finder and small tape measure in the field. After a bit of practice I didn't need the laser finder. I rarely blow an image due to focus problems where as before I routinely had issues. The longer the lens the bigger the problem.
BTW: I use the same procedure with my P1 645df and it's glass.
The new IQ backs have a live view sharpness scale and focus mask for which I am anxiously waiting.
Hope that can be of some value to you.
Ed