Ah yes, I did forget to mention a bit on how this randomness works on the programming level. If you read the OP's opening post with the quoted text, they mention the RNG but add pseudo to it. Yes a computer cannot inherently create randomness. It's an impossible feat for it to do when it's designed to be accurate. If it wasn't computers wouldn't work like they do now. As such, a random list of numbers is used. However it's not just one list, there are a great deal of lists. The calling up of the random function requires a seed to pick a list to use as the call of the function. If you don't want to be unpredictably random you'd use a predictably mutable seed or a fixed seed. I believe this is how older games used the pRNG and you tell this is the case when you can predictably have the same outcome from fresh start of a game from powering it on. Look at games that have an abusing the RNG guide. To prevent an application from having this issue you want a seed that is unpredictably mutable from the onset of the starting of the program you are running. In most cases the random seed used is the current time. This works rather well since the call to current time returns a number that is the number of seconds that have passed since a predetermined date making the result a different seed number every time you call the random function. it's still not completely random but it makes it really hard to predict the seed unless you know exactly what time random was called, how current time returns a number and how random uses a seed that might fall outside the bounds of the number of lists it has to use.
Finally after a number has been generated for use, it's however the coder wants to used it. Since this game uses percentages for success for crafting HQs, Iwouldn't see why it's not the same for atma or alex drops from FATEs. In this case how I've usually see it done is if the resulting number is less then or equal to the percentage odds where both numbers used are in the same scale. Scale begin that if the percentage is a whole number the numbers 1-100 are used.
Computer randomness is is rather complicated and this is mostly a gist of how it works. But even I as a programmer has problems with understanding all of how the random function works because the function is based on what source you are calling it from meaning that in different coding environments will used a different way to call a similar random.