Tracking Manufacturing Costs

One of the facilities in my organization uses a custom-built application for operations and manufacturing costs because they claim that certain things couldn't be tracked in JDE 9.1 (and before) and they need a detailed cost variance report to analyze the completed jobs. Is it true that JDE cannot track things such as machine down time, extra employees assigned to the job, etc.? I find it very hard to accept that a custom application is required to have this information available. I avoid JDE Financials at all costs, so I'm not familiar with the standard JDE process for tracking costs.