Using Raster Calculator Con(isnull) with ArcMap

I am using ArcMap 10.4.1 and the Raster Calculator to subtract polygons of clouds, land etc from my DEM. I use the statement:

con(isnull, Cloud, DEM) 

and set the processing extent to environments of input because otherwise I do not get me whole DEM back.

Every time I do that though, the extracted cells do not match with the extent of my polygons anymore. There is always a shift of a few meters.Cell size is same for both.

Where is the problem?