Pasternak is a traditional trade supplier with a good reputation.
amit, I just came across this beads on Etsy, maybe you could have a look. It's just vermeil, but maybe....:
https://www.etsy.com/listing/289048921/25mm-silver-italy-diamond-cut-beads?ref=shop_home_active_4
For beads like that, amti, I just have them sit over the knot. Even in really small metal bead sizes, the holes are pretty big and it would be hard to make knot big enough to stay outside the whole (and it would look odd). That necklace is really pretty!
a surgeon's knot, where you flip the strand thru twice in the same knot, worked better to create larger knots if needed for pearls with larger holes (though they don't tighten up as effortlessly as single knots do with beader's secret and are next to impossible to undo!). for tiny beads with bigger holes, though, having the bead sit over the knot seems like the best solution.