Hi Ian,
As @Dilligaf says, there are 256 different prefixes for Apple remotes to allow a mac to identify one remote from another and “pair” to that remote, hence most Apple remotes have different codes. It’s possible to change the code of a remote by holding down Play and Right (from memory) but as there are 256 possible combinations you could be there a while. 
I don’t suppose you could upload your lirc file which you have created with multiple apple remote entries in it ? You could do this with:
paste-log filename.conf
I’m researching the possibility of tweaking the lirc profile for the Apple remote to ignore the prefix bits - thus supporting all Apple remotes from one profile. In theory it should be possible if the lirc configuration file format is flexible enough.
Unfortunately I only have one apple remote (the old white kind) and I haven’t seen it since before we moved house recently… 