The WAB Impact Assessment suggests that the Ireland/Northern Ireland protocol could have a quite harmful effect on trade within the UK. I say could because it’s clear that the government isn’t really sure what the impact will be.
1 in 5 companies in Northern Ireland imports goods from GB. 1 in 20 exports to GB. Government doesn’t know how many GB companies trade with NI. Says new customs/regulatory rules will “disproportionately affect” small and micro businesses. 
Companies will have extra customs paperwork to fill in for good sent both ways accross the Irish Sea. Government says that “due to data limitations” it is not able to estimate what sort of costs businesses will have to absorb.
Agri-food goods from GB to NI will be subject to “identity, documentary and physical checks” to ensure compliance with EU rules. Govt says ”the associated costs are uncertain” and “perishable nature of many agri-food goods means that delays can have disruptive consequences.”
Manufacturers exporting from GB to NI will be subject to “risk-based” checks (documentary + physical) for compliance with EU rules. Some “may need to move certain regulatory functions to Northern Ireland or another EU member state” Yet again “associated costs are uncertain”
Impact assessment warns there is a risk that the customs/regulatory border in Irish Sea will damage “trade, business investment and consumer spending” in UK. Government could take steps to “support businesses” as cost of new checks and administration “may affect profitability”.
