> The result is the same; there's an unsightly large gap between the
> stuff on the first line before the comment marker (whether % or ^^A)
> and what's on the following line. [I'd actually noticed this first in
> a .dtx file, but used normal LaTeX syntax here for ease of
> illustration.]

Sorry, I shamefully hadn't compiled your MWE.  Here are three ways to go:

- Use the primitive \ignorespaces (in the syntax environment, active
spaces expand to normal spaces IIRC), and comment out the
end-of-lines.

- Comment the end-of-line and start the next line directly at column 0.

- Split the arguments in the output, since they don't fit in a line anyways.

  \begin{syntax}
    \cs{some_function_with_a_very_long_name:nnnnn} \ignorespaces %
      \Arg{first argument} \Arg{second argument} \ignorespaces %
      \Arg{third argument} \Arg{fourth argument} \Arg{fifth argument}

    \cs{some_function_with_a_very_long_name:nnnnn} %
\Arg{first argument} \Arg{second argument} \Arg{third argument} %
\Arg{fourth argument} \Arg{fifth argument}

    \cs{some_function_with_a_very_long_name:nnnnn}
    ~~\Arg{first argument} \Arg{second argument} \Arg{third argument}
    ~~\Arg{fourth argument} \Arg{fifth argument}
  \end{syntax}

Admittedly, none of the three "solutions" is great.  As Joseph notes,
we've gone for a single line in the l3 source.  We could perhaps add
\def\^^M{\unskip\space\ignorespaces} to the \begin{syntax} setup: this
would allow

    \cs{some_function_with_a_very_long_name:nnnnn} \
      \Arg{first argument} \Arg{second argument} \
      \Arg{third argument} \Arg{fourth argument} \
      \Arg{fifth argument}

Regards,
Bruno