At the end of loadsimplefont function in pdf_font.c, when no Widths defined in Font Dict, mupdf tries to construct hmtx from font program. The codes of getting advances of glyphs:
504:	else
505:	{
506:		fterr = FT_Set_Char_Size(face, 1000, 1000, 72, 72);
507:		if (fterr)
508:			fz_warn("freetype set character size: %s", ft_errorstring(fterr));
509:		for (i = 0; i < 256; i++)
510:		{
511:			pdf_addhmtx(fontdesc, i, i, ftwidth(fontdesc, i));
512:		}
513:	}

As descibed in FreeType2 doc, the unit of char_width and char_height in FT_Set_Char_Size is "26.6 fractional points". So, char_width and char_height should be 1000*64, not 1000.