Bode tested additional areas on the crotch of the panties and found only JonBenet’s profile. And remember the DNA found in the panties was a bodily fluid whereas on the longJohns it was skin cells. If there was no intruder then the blood drops would not have contained the profile of an unknown male, the electropherogram would have looked just like the additional tests they did on the panties.
ETA the electropherograms of Bode testing of the panties and the longJohns. http://jonbenetramsey.pbworks.com/w/file/fetch/130877799/20080108-dnaPeakDiagrams.pdf
And then there's this from Suzanna Ryan's "Trace DNA Analysis: If Your DNA Is On It Did You Really Touch It?" (2016):
“Touch DNA samples cannot be serologically tested to determine their biological source. So, unlike the blood found on a bloody knife or the saliva found on a bite mark, while forensic scientists can determine if DNA is present and sometimes determine who that DNA matches, they cannot determine if it is blood, semen, saliva, skin cells, mucous, sweat, vaginal fluid, and so on if it is submitted as a ‘Touch DNA’ swab."
Your next sentence, "If there was no intruder...," doesn't make much sense to me. Blood on top of "saliva"; blood mingled with "saliva" are, I would imagine, going to be much the same thing when they're scooped up on a swab. It's not like they took micro slices off the top of the blood drop. They probably applied some kind of solvent to it to lift it, if only distilled water.