Did you also set the physical switch on the X5 itself to MF? Also, why would you keep Auto Camera settings on in DD if you are planning to override these automatic settings? I reckon keeping these settings set to auto may be part of the problem.
I did some benchmarking earlier last week, using both DD, DJI GS Pro and Map Pilot. I found considerable differences regarding forward- and sideward overlap (particularly how these compared to the values set), but surprisingly hardly any differences in focus/ sharpness. I found that all images were relatively sharp, regardless of the application. I follow the same procedure as you did, but turning Auto settings off and the physical MF/AF switch to MF.
I must admit that the terrain in my case was relatively flat. There were some changes in elevation but no trees or other objects that could get the focus off. Likewise, I am not entirely able to state how DD performance in regard to the other applications with respect to image focus. This follows from me experiencing sincere focussing issues with Map Pilot in the past, but not seeing any of these issues this time. Hence I reckon this may partially follow from the terrain, and not necessarily from one application performing better than the other.
Although I like GS Pro a lot (it's interface is almost 1:1 comparable to DD), I do find the forced 1 image/ 5 second interval problematic. Following from our maximum flight altitude of 50m AGL, we are only limited to 3m/s when adhering to a 65/65 overlap. Using DD we can accomplish anywhere up to 5-6m/s. This does increase the area one can capture on a single battery by A LOT.