Actually, you can even run latex --output-format=pdf foo
Well, to get something useful, you have to make sure that the latex format is created with useful setting for e.g. \pdfhorigin and \pdfvorigin. If you just latex -ini latex.ltx latex --output-format=pdf sample2e you'll get a messed-up sample2e.pdf. This means, that we either have to make sure to set useful defaults for *all* formats that we dump with pdfetex or that we reactivate the config file.
Maybe the problem is that you just don't expect from inipdfetex to be initialized to DVI output format ...
Maybe, pdf*tex should defer this message until the dvi vs. pdf decision is finally decided (don't know when this is: when typesetting the first boxes or when shipping out the first page). Thomas