nrebugs,
welcome from the shadow into the light!
No way to answer your question; but lots of folks will offer "opinion". (No offense to DJU, he is braver than I.)
Too many variables(and you didn't even mention bore condition), and there is(are) usually more than one issue- so the "either or" is not a valid question; then add in that different "things" are worth more or less to the individual- and you quickly reach the conclusion that one cannot explain pricing- especially what a luger sells for at auction. JMHO!
You have pretty much answered the second part of your question with your own first purchase.
Obviously the mismatched mag was not an issue for you, nor was a questionable bore- and you bought the pistol at a reasonable price.
The "big" retailers ask pretty high prices, how high- maybe 30 to 100% more than you can buy a similar pistol for if you take your time and do your home work.
But occasionally they screw up and you can snatch a bargain, but you must be quick! Or an auction doesn't garner bids for whatever reason.
Dozens or hundreds of fellow collectors are scouring the sources for good, cheap, or sleeper luger; got to be "on your toes" .