I'm sure not expert but is it possible that Margulis overstates her case?
It seems that there are a lot of complications in how things unfold. But that doesn't mean that any of these new mechanisms are all that common or really important to many forms of life now.
They may well be very important in early times and for unicellular life now though.
I'm not sure it makes Lamark "right" if he was saying things about giraffes necks though.