There's a lot in each part of your question. Basically, the 5.5-9.5 is just to comply with local sewage laws, they're pretty uniform; conduits, treatment facility equipment, and bodies of water, worldwide pretty much need to be "about" neutral to handle the effluent stream, and 5.5 - 9.5 are pretty much what I'm used to for lab waste output requirements.
If you neutralize the API before you decompose it, you might encounter solubility problems, as a charged molecule, it remains more soluble, and reacts better with water and heat otherwise, it will precipitate or "oil out", and you might not even get it out of the tank. Double check my point, see if the first one, you apply to acids, actually applies to basic API, and vice versa.