That just means they were trying to cut costs (by reducing their storage footprint) and increase revenue (by charging a premium for photos) at the same time. I guess the brass at eBay deemed the commercial value of archiving old listings to be worth less than the cost of storing them. Remember, storage used to be very expensive, and no amount of engineering effort could decrease the cost of server racks and hard drives.
eBay Motors is separate because the process of buying a car is very different from buying knickknacks. The number of listings on eBay Motors is tiny compared to the main site, so it doesn’t even make sense that they’d split it off specifically to split up their listing database.
None of what you mention is evidence of a technical limitation.