I view large software packages like ERP systems as different from a tool. You're adopting the metaphors of the system. Sometimes those metaphors are flexible enough to accommodate some of the nuance of the origination you're in, but sometimes you strain them too much or more likely misunderstand what the system is really doing.

People who advocate for letting the ERP dictate the rules are using the phrase as a shorthand for, "If you want to customize the hell out of it you probably shouldn't use it".