The manifold, if anything, quietens down the car.
The only slight issue is that the later cars are missing a bracket for the mid pipe; its not needed. A MOT examiner seeing the unused hanger on the exhaust, might conclude the exhaust is improperly secured. I cut the bracket off the exhaust on my car (a 1996 Eunos Roadster).
My car is subject to the same emissions test as yours, which is a bit stricter than for the earlier cars. I have had the expensive misfortune of finding the aftermarket cats were marginal for later cars. It would pass with the original factory 375mm cat. When I fitted the MX5parts manifold, originally they supplied an adapter to allow me to continue to use the 375mm cat.
Then the cat failed, so I “upgraded” to a 440mm cat, and got rid of the adapter, which caused the caback to gouge the PPF.
I then swapped out the Mongoose catback for a MXparts twin exhaust. Then my trouble started. Every couple of years, the car started to fail on emissions, and a new (aftermarket) cat got the car through emissions. The specialist looking after the car was confounded. It has a very strong engine. Coilpacks, MAS all changed, and he was concluding that I was looking at a top end rebuild. The final hail Mary was to refurb the injectors, which improved things marginally. The car was starting like it had a brand new motor.
So we decided the aftermarket cats were junk. I got hold of a scrapyard factory UK 440mm cat, which cost three times as much as the aftermarket cats. The omens weren’t good. What I got looked 30 years old, with half the heatshield rusted away.
Put it on. Emissions were “perfect”, best the specialist had seen on a 1.8 Mk1.
My car, a 96 Roadster, is supposed to have the slightly higher compression later motor, like yours, but it was swapped years ago for a motor out of a 1994 RS-Limited, but its running off the 96 16-Bit ECU etc.
Based on looking at the MX5parts twin exhause compared to other systems I have fitted over the years, I would not say its the best quality system. My exhaust is louder than the previous Mongoose, but not overly so. But it does drone at motorway speeds.