Yes the rear of the car is slightly different to make it fit / work. Here’s a quote from the technical site: Packaging a retractable hardtop mechanism into a small car like the MX-5 required a new rear section of the bodyshell and new bootlid. This gives the RHT a different roofline and enlarged rear end compared to the soft top models.
This thread is confusing - what exactly are you seeing on eBay for £200?
A Mk3/NC detachable hardtop is probably around £500 or more at this time of year. It will have a heated rear window - is this the electric bit you are referring to?
The Power Retractable Hardtop or PRHT is part of the roadster and can’t be retro-fitted to a soft top (nothing is impossible but why you’d want to?) without changes to the rear tub and bootlid etc.