I believe engine capacity has a greater impact on CO2 output than number of cylinders.
So a 2.5l engine with 4cyl or 6cyl should have similar CO2 values.
What is different is that the 6cyl unit is more expensive to produce but should have other advantages: higher torque, less vibrations, better sound... all the marks of a premium brand...
I remember when Jaguar launched the X-type sedan they had a small engine with 6 cyl (2l or 2.5l).
About mass: yes, the 6cyl unit will be heavier but not by much because the cyl are smaller; however the size will be different too... but that should not become a packaging problem for a Boxster or a 911 since they have 3.4-3.8l 6cyl units now, except they want to make the cars smaller...
IMO if they go this route is because is cheaper OR they want to offer some hybrid tech so the mass and packaging differences are important...
However I will be disappointed... in order to justify the high prices they should offer 6cyl smaller units otherwise why not buy an Audi TT RS instead of a Boxster?
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There is no try. Just do.