That's because Peter is using EasyMiNT, which symlinks xaloader.prg
to /usr/bin. Then the symlink is referenced in ttytab. The idea is most
likely that you can easily select which xaaes to load by updating the
symlink. In reality it prevents you from easily booting different
versions of the kernel.
No, it does not but you must use the symlinks and aliases in proper way. For example, I do have alias for xaloader as well but I use it in combination with $SYSDIR, i.e. the link / alias points to $SYSDIR/xaaes/xaloader.prg. Problem solved for every kernel and its' repairable from TOS.