Except that you are trying to compare two different elements of the game.
In the first case (Atma) there is a static figure that determines how frequently an Atma can drop in any given FATE. This figure at least for the purposes of this discussion has been defined in the form of there being a 2% chance of the Atma dropping from any given fate, but as far as the actual programming language is concerned it is probably more likely to be defined in a manner of if a given variable is true at the completion of the FATE, then the ATMA is able to drop, what this variable happens to be is something that I couldn't even begin to hazard a guess, in fact the variable is probably different for each and every FATE in the game so as to prevent people from taking advantage of figuring out the variable in one FATE and applying the same variable to all other FATE's.
Additionally compounding the Atma problem is that the chance to gain an Atma does not carry over from one FATE to the next. In otherwords you have exactly the same percentage of a chance to gain an Atma after completing 50 FATES as you did when you first started. Completing more FATE's does not increase your odds of getting an Atma in the least bit. Doesn't hurt those odds either though.
In the second case you are comparing the Atma grind to a High Quality Synthesis Attempt. Problem here is that they are nothing alike. And unless you get 100% on the High Quality Bar, you will ALWAYS, ALWAYS have a chance to fail getting a High Quality Item, no matter how close you are to that 100%. There is a reason 100% is known as the perfect percentile.
You actually counted how many FATE's you had participated in? And you counted them to that high of a number? Do you have a life?
That statement proves that you have never been to a Casino. Gambling has absolutely nothing to do with luck (unless you are using a Slot Machine or other purely mechanical method of gambling) and has everything to do with skill in the modern day and age. Even games involving dice can be largely skill based depending on the individual practicing the game. There are several people out there who can actually control what number a die will land on to some extent. And let's not even get started on Professional Poker and the amount of that game that is skill as opposed to luck (and I am not even talking about card counting here).