PStill Use Case: PDF/X Generation on the command line:

Applies to: ALL VERSIONS 1.90.xx and newer.
 
You need also: 

- the print condition / intent name (ask your publisher)
- the matching CMYK profile for the intent

e.g. for the used "CGATS.21-2" see

https://www.color.org/registry/CGATS21_CRPC1.xalter
 
To generate PDF/X-1a (CMYK only) from any supported source (PDF, EPS, PS. PNG, JPEG, TIFF, etc.) use these options:

-v -M defaultall -d 400/300/600 -m Xoverprint -m XimgAsCMYK -M noProxyText -M keepPDFBoxes 
 -m XPDFX=CGATS.21-2 -m XPDFXVERSION=1A -m XICCProfile=/path/to/CGATS21_CRPC1.icc 
 -M cmykcolorprofile=/path/to/CGATS21_CRPC1.icc -o output.pdf input

Note: You should supply the print condition / intent as required by your publisher. 
In the above case the print condition is "CGATS.21-2" with the matching profile "CGATS21_CRPC1.icc". 
And yes, you need to supply the profile twice in the options! The first occurance is for
embedding into the resulting PDF, the second for color conversion to the color space.

Images will be downsampled to 300 dpi (color/gray images) and 600 dpi (monochrome). This is
also optional and can be controled by the -d ... option.

To generate PDF/X-1a (CMYK and Spot colors) from any PDF use these options:

-v -M defaultall -d 400/300/600 -m Xoverprint -m Xspot -M noProxyText -M keepPDFBoxes 
 -m XPDFX=CGATS.21-2 -m XPDFXVERSION=1A -m XICCProfile=/path/to/CGATS21_CRPC1.icc 
 -M cmykcolorprofile=/path/to/CGATS21_CRPC1.icc -o output.pdf input

The same as above applies here for the print condition / intent.

To generate PDF/X-3 (Gray, RGB, CMYK and Spot colors) from any PDF use these options:

-v -M defaultall -d 400/300/600 -m Xoverprint -m Xspot -M noProxyText -M keepPDFBoxes 
 -m XPDFX=CGATS.21-2 -M keepsrccolor -m XICCProfile=/path/to/CGATS21_CRPC1.icc 
 -M cmykcolorprofile=/path/to/CGATS21_CRPC1.icc -o output.pdf input

To include all fonts (even base fonts) in the result also add option "-s" after the "-M defaultall" option.
To generate 'fontless' PDF results add option "-P" after the "-M defaultall" option instead,
text will be converted to graphics/paths, output size and runtime will increase.