Agreed, unless you're ready to replace the softener with a much larger unit, your next best plan might be to run all HP functions on your auto with hard water and soften only the chemical application, if that's possible. It's also likely that the media in the softener is broken down and inhibiting flow, which may be why it's bypassed now.Ouch!
Based on your data that water softener can treat no more than 4,500 gallons. That would explain the frequent regenerations.
The softener is grossly undersized for the facility if its indeed feeding an IBA, SS bays and RO system.