When JSL encounters that line, it gives "SyntaxError: illegal character" and stops processing the file. Using the "jsl:ignore" feature does *not* change this behavior. The only workaround is to comment out the "#include"s before running JSL, and uncomment them afterwards.
Ideally, JSL should have an option to not only permit this syntax, but also interpret it as an implicit "jsl:import".
But at the very least, "jsl:ignore" should suppress this error on "#include", "#initclip", "#endinitclip", and any other such identifier ActionScript might have added since then.