Take a xtrans.pc file like:

prefix=/usr
exec_prefix=${prefix}
libdir=${exec_prefix}/lib
includedir=${prefix}/include

Name: XTrans
Description: Abstract network code for X
Version: 1.2.1
Cflags: -I${includedir} -D_BSD_SOURCE -DHAS_FCHOWN -DHAS_STICKY_DIR_BIT

and call pkg-config from a bash like (all on one line):

PKG_CONFIG_ALLOW_SYSTEM_CFLAGS=1 PKG_CONFIG_ALLOW_SYSTEM_LIBS=1 PKG_CONFIG_PATH=/sources/emb_prj/dest/usr/lib/pkgconfig PKG_CONFIG_SYSROOT_DIR=/sources/emb_prj/dest  pkg-config --cflags "xtrans"

than all I get is:
   -I/sources/emb_prj/dest/usr/include

instead of the expected:
-D_BSD_SOURCE -DHAS_FCHOWN -DHAS_STICKY_DIR_BIT -I/sources/emb_prj/dest/usr/include

The three preprocessor variable defs are missing.

The problem does NOT occur if the env. var. PKG_CONFIG_SYSROOT_DIR is not defined.

I could trace down the bug in the function 'string_list_to_string()' defined in pkg.c:

static char *
string_list_to_string (GSList *list)
{
  GSList *tmp;
  GString *str = g_string_new ("");
  char *retval;
  
  tmp = list;
  while (tmp != NULL)
    {
      char *tmpstr = (char*) tmp->data;
      if (pcsysrootdir != NULL)
        {
          if (tmpstr[0] == '-' &&
              (tmpstr[1] == 'I' ||
               tmpstr[1] == 'L'))
            {
              g_string_append_c (str, '-');
              g_string_append_c (str, tmpstr[1]);
              g_string_append (str, pcsysrootdir);
              g_string_append (str, tmpstr+2);
            }
        }
      else 
        {
          g_string_append (str, tmpstr);
        }
      g_string_append_c (str, ' ');
      
      tmp = g_slist_next (tmp);
    }

  retval = str->str;
  g_string_free (str, FALSE);

  return retval;
}

If the var. 'pcsysrootdir' is not NULL *and* the 'tmpstr' does not start with '-I' or '-L' then the string 'tmpstr' won't be appended to the result 'str'.