legends about pokemon are things people made up to explain stuff a perfect example in rl is the Kracken, in old tales it destroy ships and is "godly" for lack of better word where in reality its just a big mysterious squid, that is relativly rare to see. the same goes with pokemon, those ancient legends were used to explain it in the old days, an example in your post is latias's pkdex entry, legend says invisibility but study has proven it reflects light in certain ways, Mewtwo was created to be the most powerful pokemon thats why its stronger. Kyogre and Groudon didnt creat land and sea, those species just have a rivalry and if thet did create land and sea then where did they fight to begin with? Legends about legendaries are just old tales. Also, these "theories" differ from area to area because of culture for example kanto an hoenn say that pokemon came from another planet where as sinnoh says arceus created all. they contridicict just like differant north american tribes believe in differant spirits. really these pokemon arent godly or legendary. there just rare and not much was known back when they were thought up. But, just like in our world there are things science cant explain, deja vu, premonitions (freaky when you meet som1 in a dream an later on in real life) , and ghosts. they all exist ive seen 2/3 but science has no stand on that. things like celibis time travel in pokemon are similar. Thats the only one i cant explain with a theory.