In PvE you want the highest dps output over a long time. In PvP you don't. If you can't accept that, we will never agree on something.
Even PvE parser software is not something I like personally, as you stated out there are many variables which are going to have an effect on your total dps. The fflogs website tried to minimize unfair advantages like waiting for a big mob group before killing the boss, or destroying all 3 traps at susano eventhough only 1 is the objective and needed. But in the end it is not a tool to know if somebody is overly skilled or not, sadly often members of speedkill groups fail to adjust to other groups tactics and are wasting a lot of time in the process, because they are simply 2 greedy. With the right group you get fast clear times and that is step 1 in getting a high dps anyway, even if you perform bad.
People started to using parser as a helpful tool because they wanted to know what killed them or what type of damage physical/magical certain attacks had, but of course some people wanted to compare themselves and so the whole ranking bs began. It is fine to an extent but not so reliable as many wish it to be.
The system of SSS is since the A9S-A12S raidtier poorly implemented. The reasons are just obvious, you can beat the fights without managing to clear the dummy. The dummy requires way more uptime and optimization to your rotation than the actual fight.
I am not saying that is pointless to do SSS, it can help you test out rotations and see if you get better with it if you are on a playstation and don't have access to third party software.
A dps meter would not be a sufficient tool to judge people, atm you have to get a feeling for it to determine if a dps class performed poorly or good, like you said it is not something with just 1 variable. But adding something like this would make a lot of players believe it would be just 1 variable.