The last article is extremely misleading. It is true that there are variations of the genetic code. (Wikipedia says 32, including the usual genetic code that we have.
https://en.wikipedia.org/wiki/List_of_genetic_codes )
But the variations are minor, each has only a few changes from the most used code. For example mitochondria (that are also "we") have only 4 changes out of 64 https://en.wikipedia.org/wiki/Vertebrate_mitochondrial_code .
So the easiest explanation is that the genetic code evolved from a genetic code ancestor. Moreover, our genetic code is probably not the original code. IIRC the guess is that initially it has only 16 slots. These slots are visible as some big squares in the curren table, but some of these slots are divided now.
Most of the time a change in the genetic code is catastrophic, so it's not easy to change it. But it may be possible if it changes one aminoacidic by a similar one, or if you are extremely lucky. In the table all the changes are in mitochondria/bacteria/archaea, not in animals or plants. Since they are small, they have bigger numbers and faster generations, so they have a bigger chance of a lucky random mutation.
In particular, 12 of the 32 genetic codes in the list are variations in mitochondrial code. All the mitocondria are very similar. The incorporation of mitocondrial was a very strange lucky event. Nobody think that the 12 variants of mitochondria appear independently, each one in its own tree of life, and were absorbed later independently.