Hi, I had the factory fit the mudguard when my M3W had its first service. All painless if expensive. Six months later what I can only assume were some bolts that sit proud of the mudguard, had worn holes in the rear plastic liner over the rear wheel. It was replaced under warranty and the bolts reworked. So when doing this job yourself make sure that the finished mudguard sits well inside the rear plastic liner.
Yes, the factory mudguard needs careful fitting to ensure that the bolts do not interfere with either the boot liner or the tyre. The instruction leaflet makes it look easy, but I found that I couldn't just follow the diagram without running into those interference problems. In the end, I used low profile M6 ‘gutter bolts’ with the threads cut to 'just long enough' length to gain a little more clearance. Don't worry, I used nyloc nuts, not those horrid square ones.

The bolt heads may be fitted either on the inside or outside dependant on which side needs the most clearance. It's important to take your time and will involve some trial fits of the boot liner while lying underneath shining your torch on the critical area.
The factory mudguard is quite short (being a Caterham front wheel mudguard...) so it's also worth considering the addition of a rubber skirt to extend the length of the mudguard by around 15cm (especially at the rear) before it's fitted.