The error that you are seeing is:

Use --in to specify a Skyline document to open

The Skyline command line does require that you either user the "--in=" argument to tell Skyline to read a particular file, or "--new=" argument to tell Skyline to create a new document with the default settings.

I was able to successfully import your transition list, but I had to use the "--batch-commands" argument to specify a file with several lines of commands.

This is necessary because if you try to do it all in a single command line, Skyline will try to import the transition list into the current document before Skyline has opened the document that you specified with the "--in=" argument, so the settings will be wrong.

I got your transition list to work using the attached files, and the command line:

skylinerunner --batch-commands=commands.txt

The commands.txt file that I attached has the following lines in it:

--in=blank.sky
--import-transition-list=test_tl.csv 
--out=foo.sky

This tells Skyline to open the file "blank.sky", then import the transition list and then save it as "foo.sky".
-- Nick

so when I import the attached transition list into skyline by hand skyline calculates the precursor isotopic envelope ions. (The M0 is in the file and skyline calculates the M1-Mn, as usual).

When I import this transition list using skylinerunner it does not calculate the precursor isotopic envelope correctly, instead it generates the festival of excitement in the attached image. Also attached is the skylinerunner batch command file.