Richard Stallman wrote:
>     If we quote emerge-command and the various emerge-*-program, we in
>     effect disallow them to be shell commands with switches.  Is that
>     reasonable?  If it is, then we should quote the programs.
>
> If that's what these variables do, their values should not be quoted,
> so that they can include some arguments.
>   

Ok.

>     > - defcustom explicit-bash-args
>
> Since that exists only to be sent as arguments,
> it should not be quoted.  The user will put in whatever
> quoting is called for.
>
>   

That is a misunderstanding. It is the variable prog inside that 
defcustom that should be quoted with shell-quote-argument. prog must 
point to a file so there is no problem here.

I have attached a patch.