Adi, I do not have a strong feeling for what software is best for controlling the motor. I seem to recall that I did some quick testing of Helicon Remote on my Android tablet and found that it worked as well as any, better than most. Because you've already had success with it, I suggest to keep using it.
CANON EF 70-200L is such one, so it should work without any limits.
There are always limits. In this case the limit will be on stack depth.
When you step focus by changing the lens-to-subject distance, there is no hard limit on stack depth. If your subject is 4 mm deep and you're shooting with a 10X NA 0.25 objective at 0.005mm step size, you just shoot 800 frames. It takes a long time, but it works well.
In contrast, when you step focus by internally altering focus of the rear lens, there is a hard limit that is imposed by the close focus distance of that rear lens. For example if the rear lens will only focus as close as "1 meter", then at 10X NA 0.25 your stack depth will be limited to only about 0.4 mm, say 80 frames.
At higher magnifications there is also a soft limit imposed by added aberrations, as discussed in the other thread.
--Rik
