Equipped with big brains and sharp stone tools, humans
appeared as being the masters of their territory but they dwelt in constant fear of predators, rarely hunted large game and subsisted mainly by gathering plants, scooping up insects and eating the carrion left behind by other more powerful carnivores
Option Elimination -
A. appeared as being the masters of their territory - avoid the usage of "being" as a modifier as it creates meaning issues. Moreover, "appeared as" is not the preferred usage. The usage of "humans appeared" - the past is wrong. Think of it as if the author of the sentence has to go back in the Stone Age and watch the human actions or if there were some high-definition cameras fitted in the Stone Age and no one watched the recording and said they appeared blah blah. Does this sound ridiculous? Right? Yes. That is why the usage of the past in this case is incorrect. The easier way to understand it is that the sentence is trying to say that humans were perceived or seemed to be the masters and that perception or the observation is still happening in the present until writing this sentence, thus "appear to have been" is correct."
For example, The suspect appears to have been at the crime scene. Meaning that there is evidence or indication that the suspect was present at the crime scene, and this belief or understanding remains till we write this sentence.
B. appear to have been masters of their territory - ok. The simple present "appears" communicates the current belief or understanding about the past event.
C. appeared as masters of their territory - the same issue as explained in A with the past tense.
D. appeared to have been mastering their territory - "appeared" here is the past tense" "to have been" conveys that this belief or understanding of human beings' masters occurred in the past.
E. appeared as to have been masters of their territory - the same issues with the past "appeared."