If you read J-300 more carefully, you'll see that the Kodak recommendation to neutralize stop baths is for their undiluted concentrate (which is almost pure acid), not for the working solution. The document is not nearly as clear about this as it could be. Dumping used (especially well used) stop down the drain should be no problem. However, one can easily neutralize both stop and developer to a degree by mixing them together before discarding as you note. This is pretty easy to do for printing sessions, since they both have about the same lifespan. When the developer or stop dies, just mix the two together and dump. Even if you don't neutralize, using copious amounts of water will dilute either to just about neutral really fast.
Good to know all the details. I suspected as much about the silver in fixer, but never knew the details.
Perhaps those of you who take their fixer to a hazmat facilitly could comment on my concern, which is that the hazmat people don't really know what to do with used fixer. The guys I dropped my used fixer off to had no idea what silver recovery was and treated the used fixer as if it were highly toxic (rubber gloves and masks!). Some spilled in the back of my truck and they seemed horrified that I just wiped it up with a grease rag and rinsed it with water. If I though that my used fix would get the silver extracted from it and recycled, I would certainly take the time to make the trip to the hazmat facility every so often. I just don't think it does. I'm still looking for a lab or college darkroom that has a silver-recovery unit.
As for selenium toner, I've been on my soapbox here enough lately about replenishment instead of discarding lately that anyone interested in what I do can easily find it with a search. I never discard selenium toner.