If the bass meets all your criteria, feels, sounds, and looks good and/or satisfactory, and you were happy with the price, then I say keep it despite the few issues you had with it.
Maybe don't buy from that retailer again, though.
[Edit] I see that it's a natural Ash Lefty. I'm inclined to think that it is not likely you'll find another one like it for a better price. That's a pretty rare bass as it is.
I've had some time to think about it and have decided to keep it, as you say despite the issues I've had with the bass I still really like it and it may be difficult to find another Natural Lefty one very easily.
I'm really not sure about the 2010 serial number on the neck, despite the dullish finish of the frets I actually think it is a new neck, the back of it seems very clean and smooth (from newness not from playing/wear). I took the strings off and the nut is completely clean and neither the nut, frets or fingerboard show any signs of wear.
I also removed the neck to see if there were any date stamps on the body or neck but unfortunately not, but there were a few bits of newish looking sawdust in the neck pocket. I cleaned the frets which didn't need much effort into getting them back to being bright and shiny and I applied some Dunlop Lemon Oil to the fingerboard so the neck is looking really nice now. After that a quick clean of the bridge and a new set of D'Addario ProSteels and the bass is looking and playing really good. The rest of the night I've spent playing it and going through all the tonal options. I'm not sure whether the treble control works as it should though, with the treble control fully off there only seems to very small sweep of the control before the treble cuts in?
Looking forward to gigging with it now but our next show is a few weeks away yet.