IT works fine, I have used it on 1.4 with Glide64 and it was fine. Quest 64 on those specifications ****ed up the game if you used the default video drivers. Brian's hair goes all white, his colours are screwed up, and the texturing is messed. Also most attacks like Fire Ball and Wind Cutter get inverted colours. However, back then Glide64 fixed this. Now with 1.6, that problem is nuked completely.
I dunno bout Perfect Dark working, because I already have in on n64. I got Perfect Dark mode and most of the cheats, I just need to beat WAR! on Perfect Agent.