Simply not true - you shouldn't lose any seat assignments (those are a function of the reservation, not the ticket) and it is of course perfectly possible to do online checkin with a paper ticket.

On reflection I don't think the no-show penalty really matters if it's the last segment - what the rules say is that if you want to reschedule after a no-show then they charge a US$125 fee, but in your case you're just throwing away the rest of the ticket (it's the last segment) so I wouldn't worry about it. Try to get the LHR-NBO departure on the same calendar day as your arrival from MIA to mitigate the huge UK air departure tax.