Again, the tired old advice of dynos is invoked again - the actual numbers are not as important as the IMPROVEMENTS. The ONLY valid comparison is to strap down a stock LNF Cobalt, run it, then strap down an LNF Kappa and run it. THEN compare the stock numbers. That said, some thoughts;
1) The mig welder tip mod (known as "the pill") will NOT hold higher boost levels, but rather it allows the turbo to spool up quicker and spike high boost. Once the pressures equalize across the orifice, boost levels are whatever the car and tune can produce. I know - I have that mod.
2) Cobalts have electric power steering, not belt driven like the LNF. That is part of the apparent whp differences.
3) The most highly massaged drive train will not produce a 6.5% loss. There are just too many places to have losses. This is such an important number in racing that race shops will spend endless hours going after 1-2 point improvements. NASCAR teams have dynos set up to massage gearboxes, diffs, even u-joints and axle bearings. Been there, seen that. They get pretty excited when they get in the single digits.
4) There is a LOT of "dyno racing" in the Cobalt/HHR communities. A little reading and a few PMs will expose a bunch of ...... umm ............ optimism.
5) Every time I have seen manual box cars dyno tested, it was usually in fourth gear as that is normally a 1:1 ratio in 4 and 5 speed boxes. Why Cobalts would be run in third is odd. It may be a clutch issue as Cobalts and HHRs are known for smoking clutches once they start getting near 300whp.
6) For a given power output, a Cobalt will almost always out drag an LNF to 60 as Kappas have to shift at 57 (assuming a 6200 rpm fuel cut off) and Cobalts go over 60 in second.