NetWare virtualized on Xen does not use DOS, nor does it use the NetWare boot loader (nwloader.sys). It uses the Xen loader (xnloader.sys) to load the operating system. The Xen loader is similar to NetWare boot loader in functionality. It boots NetWare, then passes its commands to Xen as well as providing some of the interfaces between Xen and NetWare.
Therefore, when you want to start the server with specific command line switches, such as -nl or -ns, you should enter these commands at the Xen console when starting the server or put the commands in the config.nw file rather than the autoexec.bat file.