I have had good success running a few jobs generating orthos and DEMs in batch mode and setting coordinate systems with build 1985. This is very nice for the color correction step, since it takes several hours on my machine with 1000 - 2000 images.
One thing still lacking is ability to control cell center/corner coordinates. This is critical to generate concurrent rasters (exactly overlapping cells), which is important for accurate surface comparison.
The simplest way that I can think of to implement that would be to round the DEM extent/corners to the resolution of the DEM (so that if for instance I select a 1 m cell size, the bounds would be rounded to the nearest integer, if I select a 0.5 meter cell size, the bounds would be rounded to the nearest 0.5 m, if I set a 0.1 degree cell size my bounds are set to the nearest 0.1 degree... etc.
The default resolution (0 in current beta) could be left as a way to not implement any rounding and use the maximum resolution from the data.
The other way I can think of would be to add an option (like a checkbox + value field) to specify the rounding interval for cell corners. If the box is unchecked, then default bounds would be used. Either of these options don't seem like they would limit current functionality at all.