The only thing that you have to watch for is that /programs{0,1} parititions are set rw/ro by hijack, but not by the player software. This is because hijack remounts all currently mounted filesystems whereas the player software uses shell scripts that only know about official empeg partitions,
Of course, this only affects those who have the /programs{0,1} partitions formatted to begin with. Editing the ro shell script to ensure that these partitions would get remounted ro in these circumstances would be trivial.