I think it is your right to raise your concerns with the store and then with the manufacturer, if you feel that is necessary.
I don't know why the finish crack happens there, but the instruments I have that are finish cracked in that spot all sound great and have no other issues.
I have read some interesting pronouncements in this thread as to why this thing happens in some bolt on neck basses.
I have 19 bolt on neck basses (I know.. another story)- Fenders, EBMM, G & L, Squier, Gibson. 1956 to 2013. Poly and nitro. MIA, MIJ, Indonesian, MIM. Tight neck pocket/ not so tight neck pocket.
I checked all my basses just now to see which was cracked and which wasn't before writing this post. I knew some were but couldn't remember exactly which ones, that's how much I think about the issue.
Three have a superficial crack in the finish in the same spot as your pic- they are all beautiful playing and sounding basses.
These are
82 Fullerton 57 P RI- original white nitro over ash, neck pocket tight as a fishes.
04 MIM Standard Jazz- original poly over alder, neck pocket tight as a fishes. Really hard to get this one out.
73 Telecaster Bass- original thick poly over ash, neck pocket with a mm or two gap each side and a three bolt to boot. A classic 70s Fender but the neck is very stable and she sustains for days if I want it to.
So on my sample, I see it in nitro and two different poly finishes, I see it in alder and ash bodies, I see it in three and 4 bolt systems, I see it in tight neck pockets and not so tight neck pockets. I see it in US and non US builds.
I see it in cheaper builds built with an ultra tight neck pocket (MIM) and more acclaimed ones (82 Fullerton).
Where I don't see it is also interesting. I have 16 that haven't cracked that have tight neck pockets (yes even the 70s Fenders). These include 56 nitro over ash, 69 nitro over ash, 73 poly over alder, 74 nitro over maple, 75 poly over ash, 82 nito over maple and a number of fairly recent polt over alder and ash basses.
I doubt you can be assured by some of the posts here that it as a result of a tight neck pocket and that it is an indication of a superior build.
I think you can be assured that it will not impact the performance of the instrument negatively. Have it checked out to make sure it is not structural and then make your decision as to how you wish to proceed.