Hey there, actually that's pretty normal since Presonus doesn't support for Logic ^^
The faderport 8 native integration is for S1 which means all the buttons you see will be perfectly mapped on S1 but when you use the mackie universal mode for other daw or HUI for protools, then might act a bit differently so the marker button may not do what it does on S1.
The thing is FP8 remains a midi controller and you should be able, if logic allows it, to map a button to "add a marker" function . Maybe you should google that, i don't know logic at all sorry.
Hope this might help,