Thank you for the sample and for detailed explanation.
Tested with current LibRaw 0.20(beta):
dcraw_emu produces correct pgm file
dcraw_emu -T makes correct tiff file.
So, LibRaw::dcraw_process() and all previous steps are OK.

mem_image_sample.c fails to produce correct results, the problem not in LibRaw::dcraw_make_mem_image() (it is also correct, see below), but in sample source code:

1) write_ppm() do not handle img->colors != 3 case and just returns. This is expected, but need to be fixed.

2) write_jpeg() do not check for colors count, but assumes that 3-color data passed that is wrong.
Quick fixes:
A. replace
cinfo.in_color_space = JCS_RGB; /* colorspace of input image */
with
cinfo.in_color_space = img->colors==3?JCS_RGB:JCS_GRAYSCALE; /* colorspace of input image */

B. replace:
row_stride = img->width * 3; /* JSAMPLEs per row in image_buffer */
with:
row_stride = img->width * img->colors; /* JSAMPLEs per row in image_buffer */

Fixed version will be uploaded to github soon (likely tomorrow, we want to fix write_ppm sample code too).

Here are processing results (pgm file from dcraw_emu and .jpg from fixed mem_image_sample): https://www.dropbox.com/sh/a6aksx5opyzeeyv/AACG3f9GCZ703UksKjc5H5Rta?dl=0