Hi Ludwigs3rd, The intonation could be affected, but its nowhere as critical on bass as say lead guitar, The other problem could be undue stress on one side of the neck if the error is large enough. If you are happy with it why not keep it (The price was certainly right)
Better the devil you know etc, etc, Keep your eye on the neck and if you see any minor changes try the business card trick before any major developments. Otherwise from your comments it sounds fine. I must say that Peavey are not associated with poor workmanship as a rule. (In my experience that is) If the gap bugs you get some carpenters wood filler of the appropriate colour and fill the gap
Fenderphil