You can't pass filesets to operating system commands. The best you can do is use the apply task to invoke the "cp" command on each file as follows:
<apply executable="cp">
<srcfile/>
<targetfile/>
<fileset dir="src" includes="*.txt"/>
<globmapper from="*.txt" to="output/*.txt"/>
</apply>
But, I don't really understand why you couldn't combine the copy task with chmod, it would be most efficient:
<copy todir="output">
<fileset dir="src" includes="*.txt"/>
</copy>
<chmod perm="700">
<fileset dir="output" includes="*.txt"/>
</chmod>