Producing non-square pixels or reprojected results with MapServer WCS does not work with tileindexed layers. The issue is described in the email:
http://lists.umn.edu/cgi-bin/wa?A2=ind0702&L=mapserver-users&T=0&F=&S=&P=852)
With the patch, I can make GetCoverage? requests on a tileindex of DTED files with resolutions (or dimensions) not necesseraly a multiple of the original resolution, or into another projection system.
The fix consists of adding the following lines after msMapComputeGeotransform, as it's done in mapdraw.c
/* Do we need to fake out stuff for rotated support? */
if( map->gt.need_geotransform )
msMapSetFakedExtent( map );