Cheaper: we got rid of the supplier mounting, so even counting the BOM of the new box and manifold, we saved about 5-10%

Worse performance: The extra connectors on the manifold increased the total volume the sample passed through, which gave a lower resolution (this was a chromatography system). Nothing that wouldn't pass spec, but visibly degraded compared to the original system. There's also more potential for minor leaks because with the manifold you now have an additional 12 connection points to worry about

Increase tolerances to reduce cost at scale, sometimes doesn't fit perfectly or requires a little jiggling to line up right.

But now you can't do the jiggle or try to manually quickly realign it, instead you need to call a tech to do it for X bucks and a wait time of longer than a few seconds.