I don't think Minis are that bad to IVA. There's an overlap between factory production & the IVA's predecessor: SVA. The test is about compliance with the same basic C&U regs. Hence rolled exhaust & bumper ends etc.
One observation. If the refusal to issue an updated V5 precedes the VOSA inspection then it can't have been because of anything that was only discovered through that inspection, such as holes in the boot.