Well theories about accidental or deliberate contamination seem to me as plausible and possible as the 'intimate mix' theory presented at trial which also required SC to remove the silencer and return it to the cupboard before shooting herself.
I would like to think that had I been part of the defence team I would have recognised that this was by far the strongest evidence against JB and really needed to go under the microscope so to speak. What first struck me was how come the blood in the silencer was able to turn up blood groups other exhibits couldn't? For example the outside of the rifle contained a number of stains, which appear to have been of a similar quantity, also on a non-porous material and yet it was only possible to determine the blood was human in origin. Blood on the rifle was also arguably of better quality not being subjected to firearm discharge and blood removed and tested before it entered the cyanoacrylate fuming chamber and exposed to humidity.
The defence didn't visit the lab instead relied upon their expert to who reported back via 2 letters all of which seem to have been taken at face value without any questions asked.
Perhaps, as you suggest Nevill deposited a small amount of blood while he was cleaning the moderator and Junes was then added to that when she was shot. Putting aside the issue of NBs blood being older and degrading in quality, this is still a fanciful explanation but it may have caused some doubt about the results in the minds of the jury had the blood been the only evidence.
I don't see how the defence could have explained accidental paint contamination and fresh scratch marks though, what the defence could only have been suggesting to the jury is a deliberate frame meaning that an individual or several people were attempting to pervert the course of justice, an offence so serious it carries a maximum sentence of life. This would seem to apply to scientists who you are accusing of fudging their results, what motivation would they have for this and how could they know that the defence wouldn't be able to replicate their tests and expose their shoddy work?
Sometimes when the prosecution has a strong piece of evidence, the defence will prefer not to put too much weight on it and hope the jury don't either. I think the defence had little option but to take the bone thrown to them by the prosecution or risk looking desperate and give Arlidge extra ammunition for his closing speech.
PS: I'm not a scientist but the other blood stains were on porous materials, could dyes and bleaches in the fabric be responsible for them not yielding the same results? I've no idea.