> 
> And secondly the other method (using VRTs) how would one then automate that
> (to do, say 1000 tiles in a script).  The editing of the VRT would be the
> tricky part.

sed "s/<ColorInterp>Alpha<\/ColorInterp>//" should do it

But actually I think that if you just want to mosaic files in the same 
projection you could also use gdalbuildvrt
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