The fact that Russian aviation failed to train (or even require training for that apparently) is absurd, the fact that the EU allowed planes to travel with TCAS but not with pilots that had the most basic understanding of TCAS is a sad example of the results of checkmark based safety.
As even this article acknowledges, TCAS as a system makes no sense of any kind if it can be countermanded by someone other than the pilot. There is no use case for TCAS that makes anything other than "do what it says, a fast as possible" have any value at all. Disobeying TCAS because of ATC is no different than ignoring a stall warning because ATC told you to climb.