So how do you find out it is running less efficent, if the WU is always running 8 hours?

In your Account page, Computers, Details, Application details, Average Processing Rate (APR).
The number of Floating Operations performed each second. The higher, the better (ie, the more numbers crunched per hour, day, week etc).
So far it's looking less efficient, but only by a small amount- about 0.6% at this stage (at least on my system- those with more cores & threads the impacts will probably be greater). However, we would need to run the same Tasks that were processed using the other Applications on this Application for a true comparison- the present Tasks may be "chewier" than the previous ones, and may have run even slower on the previous Application than they do on this new one.

The Rosetta/L3 cache issue has been discussed quite a lot over at the Microbiome Immunity Project (MIP) forums on World Community Grid, a project which also uses Rosetta.
Running more than 1 WU per every 5 MB of L3 cache resulted in increase runtime for all tasks running (non-Rosetta too), which results in loss of efficiency considering the increase in runtime and constant electricity usage. One of the MIP scientists said they were aware of the issue and were looking into it, but this was years ago by now.