I would assume you will be sold a Logic 8 Full version serial and then the Logic 9 upgrade serial...
How legal that is? Well, it's perfectly legal so long as both serials are not currently being used by anyone else at the same time... as essentially the seller is selling you both L8 full and L9 upgrade at the same time.Where he got them from? If it's not a new unopened pack.. then who knows.. You could ask him but whether or not you get an honest answer.. is, well.. how ebay works!
Deleting the app and reinstalling, isn't going to help... and unless you do that full complete uninstall I linked to earlier... then in reality, you are just spinning wheels at best. Not that a full uninstall may actually help more but it stands a better chance of working than simply removing/deleting the app from the applications folder.
Also, I wouldn't be concerned with the bit about...
"Not only that, but you're still able to proceed with future upgrades."
...as it looks like there will be no further upgrade pricing discounts as such. When you purchase L9 from the app store you are essentially buying the full license each time... as no serials are required. I would expect the next major version of Logic to be exactly the same.... You just buy it for the one amount.., and it installs as a full version. It makes no difference if you have an earlier one installed or not... and there is and will be no upgrade pricing... as the full version costs less now, than the upgrade pricing was for the L9 upgrade from L8.
Finally, while I hope you do get a full refund from Apple, if that's how things turn out... make sure you deal with that first before spending more money on the Boxed set... so you don't end up double paying for everything.