" how does this not suggest a different gene signature...."
1. Mitochondria are simply parasite bacteria that were incorporated into cells a few billion years ago and today exist as independent organelles that still contain remnants of the circular bacterial chromosome.  That is the DNA these two studies looked at.   In the incorporation process most of the bacterial DNA was lost or moved into the nuclear DNA.  So, there is very little DNA left in the mitochondria and that DNA has nothing whatsoever to do with the current nuclear DNA.  Mitochondria are only inherited from mom.  Crossovers and recombination that are routine in nuclear DNA do not exist in mitochondrial DNA.  Dad makes zero contribution to mitochondria (usually).  Honey bee mitochondria only have 13 protein coding genes left.  Humans have the same 13 protein coding genes in their mitochondria.

2. Much of the answer to your question has to do with statistics.  Go get a good entry level college text book on statistics.  This forum is not an appropriate place to teach or learn statistics.  Half Price books very often has such a book for a few bucks.  Once you understand statistics it is obvious why I said that the results reported are the expected results and any other results would be near impossible because they would be so improbable.

3. You can do much the same studies in male mammals using the Y chromosome as can be done in females using mitochondria.  These studies show that about 0.5% of the humans alive today are direct descendants of Genghis Khan or his very close male relatives all on the paternal side.  Of course Khan lived and fought his wars from Mongolia and the steppes of Asia clear over to eastern Europe.  But, his Y chromosome moved far and wide over 1000 years ago.  So, while most of his descendants today live close to the areas he was in some are very far removed.  Those who are far removed often show no DNA ancestry at all of being oriental.  All the rest of Khan's DNA has long since been swapped out for the DNA of the new area and this has happened in only roughly 30 generations.  That is fewer generations than some of those feral bees have to have existed unbroken on the female line based on their mitochondrial genotype.  Those female bee lines have had lots and lots of time to totally swap out any nuclear DNA that was originally associated with those mitochondria.

4.  Those same studies cited are often argued by bee guys to claim that our commercial bees lack genetic diversity with the implication that domestics are harmfully inbred.  This is nonsense.  I have talked to several PhDs in genetics on exactly this topic and every one of them says that these results have nothing to say at all about the amount of inbreeding being harmful and further the experimental results clearly show that there is no harmful commercial inbreeding.

We simply need to get over once and for all thinking that mitochondria tell us anything at all beyond the obvious fact that there is an unbroken female line.  Pretty much the rest of the DNA world that works with other species figured that out 30 years ago when they started to get a little grasp of what the nuclear DNA was all about.  Unfortunately due to technical issues in working with honey bee DNA we know about as much about it today as we knew in many other plant, fish and animal species between 1995 and 2000.  And due to these difficulties when there are a lot easier places to work that will yield faster results and the low economic importance of honey bees I am not expecting fast results even thou we have much improved technology today even versus a couple of years ago.

Dick

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