Welcome to the forum, from the Derbyshire peak district.
I don't think the pillion insert thingy will ever become comfortable. Especially on a long ride.
I keep meaning to do something about it myself, but it's only really the longer runs where it gets proper annoying for me, and so far, I haven't tended to do all that many long (non-stop) trips so I keep not getting round to resolving the issue.
I guess it will be just a case of peeling back the vinyl covering and sorting out the padding and then rolling the vinyl back etc... but it could also be influenced by the hard plastic moulding part of the unit. I must get round to doing something this winter, or before I do another proper long day in the saddle.