@Radius: I guess so? I just happened to flick Cydia on this morning though and it told me there was an update available for Retroarch so I upgraded to it, perhaps the update has only gone live on the repo today as I checked a day or two ago and there was nothing? Anyway it’s working now and I’m extremely happy 
@Nerve: after updating to the latest build from the Retroarch Cydia repo it does seem to remove individual bind keys from the list, however, by using the “User 1 Bind All” option which is the 4th option after you go into the “Input User 1 Binds” menu I was able to get my Stratus working! I did encounter a couple of bugs though which were weird, the Stratus wouldn’t always connect first time so I made sure it was working by first trying an app/game that already worked to make sure it was properly connected, also when mapping the buttons/Dpad/analogues, if you missed out binding any keys it would sometimes not let you bind others as they would be removed from the process, an example is I decided not to map a key for “select” so “start” wouldn’t show as it was cycling through all the other keys/directions to map! I also had a problem where it would let me map all the analogues except “right” on the right stick but again that was down to me missing mapping one of the right triggers such as R2 or something, bizarre! Anyway I managed to fumble my way through it in the end and mapped certain buttons to a key or trigger twice which aren’t used such as start and also right trigger 2 to the same button as they won’t interfere on N64 stuff! anyway I hope that’s not too confusing a description, I’ve tried to make it as easy as possible to understand! After this I think you can also map individual control layouts for specific cores and even games but so far I’ve tried N64, Playstation and Saturn and they all work great 
Oh and no, you don’t need Controllers For All, that’s for mapping other controllers such as PS3 or Xbox to mimic an MFi controller as far as I know, no need for us though as ours work right out of the box 
Good luck!