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.
I think theories re innocent contamination are unlikely eg:
1. Anyone who handled the silencer from manufacturing up until 6th Aug accidentally depositing blood inside.
I think theories re deliberate contamination are unlikely eg:
2. Relatives using SC's menstrual stained underwear as a source of blood
3. RWB dobbing his blood inside. How would he know he shared SC's blood groups: enzymes and proteins?
4. Police deliberately contaminating from 1 of 3 vials containing SC's blood passed to the police from Dr V/pm and stored in soc fridge at Chelmsford HQ.
I think the theory put forward by the defence is unlikely:
5. None of NB's gsw's were considered contact and only 1 sustained by June was considered a possible contact but it was thought "unlikely". Given the. 22 rifle, low velocity ammo and silencer make back spatter unlikely this would seem to rule out the 'intimate mix' theory which also required SC to detach the silencer and return to the cupboard before taking her own life.
IMO I think the lab colluded with the police to fabricate the blood/silencer evidence as its the explanation that stacks up.