EM5214 - Penalties: formal determinations: cost-effectiveness
Where your enquiry includes periods before penalties under FA07/Sch24 or FA08/Sch41 were applicable, issuing formal penalty determinations will inevitably be more resource-intensive than including the penalties in a contract settlement.
Where the only penalties included in the settlement are under FA07/Sch24 or FA08/Sch41, there may be no advantage to be gained by entering into a contract settlement.
Either way, you should not normally settle your enquiry by contract settlement, unless this is easier than issuing formal notices.
Follow the guidance at EM6002 for the cost effectiveness of settlement via a contract.