In case anyone ever has the same issue as I did, in my case the printer had the Z bed minimum (#define Z_MIN_POS in the Marlin Config file) set to -5. This caused an issue with the mesh leveling having an offset of ~5. So if you also have a large offset, it's worth checking this setting in the firmware.
Posts made by Thommm
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RE: Substantial z offset after mesh levelposted in General Discussion