RIPE Atlas is primarily designed for INTERnet measurements, not Intranet.
Emphasize on the "primarily", that doesn't directly mean private measurements shouldn't exist.
If one has a problem with open-data philosophy, he shouldn't participate in this project.
The existence of a token system already incentivizes contributing, without just making good public measurements that contribute back open data.
It shouldn't be necessary to run the same measurement multiple times. For what reason?
Because things change in the wild?
There's only one exception
Well... So in addition to lack of a good basis in principle, non-private measurements might also pose an unnecessary additional information leakage. In addition to that, many measurements are just absolutely useless for others. I am also certain there are people who only contribute (by hosting a probe) for that reason - running a few private measurements.