As a fairly strict 4-dimensionalist (xyz+t), I’d have to say that Bell’s Theorem only seems to support the co-entanglement of wave functions (as across a wavefront), but not of atoms. I don’t believe that it will ever be properly shown to apply to free protons, for example, which are essentially positive ions of hydrogen.
Also, I don’t believe that most observed “violations” of Bell’s inequalities should be seen as emblematic of non-locality, but instead should be recognised as predeterminations imposed by each experiment’s “entanglement” process or parameters (i.e. generating, lensing, mirroring, polarising, detecting, etc.).
That being said, however, I do think that it’s possible to demonstrate apparent non-local behaviour across cohort waveforms, ostensibly as a coherence function of wavefront integrity, but that is a different sort of beast.
As our main platform for particular non-locality, even in its most corpuscular form, I believe that gravity deserves some reinvigorated attention.
Anyway, here’s a brief, bold paper from C. S. Unnikrishnan on proving the absence of nonlocality in quantum physics.