Okay, after reading through Bob's feedback - which was highly detailed and extremely helpful - I've revised with the following:
- It now tunnels proton/neutron pairs rather than just protons. This doesn't fix the isotope issue (see below) but makes the math a hell of a lot easier as well as making it plausible they would line the test chamber with lead, as the primary issue is no longer beta decay but gamma radiation emitted by the unlikely isotopes this produces.
- Probabilistic effects: Bob pointed out that if the tunnelling was 'random', as I stated, it should result in an even smattering of transmuted particles throughout the area (I note that since the quantity of material inside 1477 is relatively small it would probably be hard to notice any change), and some particles would be transmuted more than once, resulting in a mix of elements. I've handwaved this a bit by explicitly mentioning that any given atom in the exterior radius only receives as many subatomic particles as are lost by any given atom in the oven (quite how they would tell this is still a problem), and also name-checked Holben's beloved two-body decay, which seems to offer a solution for the 'clumping' I want.
- Molecule vs atom: I did indeed mean for individual atoms to gain new subatomic particles, not just the molecule generally; hopefully the 'clumping' also fixes the issue Bob pointed out whereby one atom in a molecule might be transmuted but not others.
- I have fully embraced the isotopes and made them a central part of the SCP. The heap of Be2Na is out of the picture as both end up decaying into oxygen after a few minutes, but to my delight calcium transmuted in the fashion I wanted actually reaches stability when it reaches titanium, rather than vanadium, and the paper and ink both transmute in a stable fashion.
- The astatine issue has hopefully been resolved by the clumping explanation and the fact that the primary risk is now explicitly gamma radiation. Not sure if I'd already saved it by the time Bob read it through, but last night I also made it clearer that transmutation of the test chamber walls had never been a problem in testing before due to the fact that at higher settings the effective radius is that much smaller. If it's still a problem I'll make it clear that this was something they worked out as a result of the incident rather than beforehand.
Incidentally I've picked up on another issue - when initially writing this I assumed that excess electrons would be emitted as beta radiation, but that doesn't seem to be correct. Instead, it appears virtually everything affected by the oven would be ionised to hell and back. I've given this a brief mention in the article but am unsure whether this has further corollaries I need to address.