Don't know anything about the specifics, but at a high level I'd guess the
difference is between programming the rest of the system to accept the new
box, or programming the new box to pretend to be the old one.
There are pros and cons of both approaches, but it is possible eg that the
factory module can't be reprogrammed to pretend to be another and so the
dealer workflow is to reprogram the whole system, but somebody has made an
aftermarket modification (or a compatible box) which does allow 'pretending'.
If there is any calibration required, perhaps it transfers the calibration
from the old box to the new box, rather than doing a full recalibration as
the dealer flow would do.
But maybe this aftermarket route doesn't help you if your module is so badly
damaged that it isn't responding at all which would prevent it being cloned
or the calibration read out.
But as I say I have no experience of this, this is just guesswork.
Theo