"Are organizational differences in common areas like inventory control and accounting actually adding any value?"

Absolutely! That's the entire basis for my business. If there was anything remotely close to what my customers have been asking for, I'd be out selling it.

"In most cases I think they could be standardized without any long-term loss."

That's why you and I hack and our customers run businesses. It took me a long time to learn it, but now I listen to what they say, not what I think.