We're not saying "is."
We're saying "He's gone there many times."
"He's" could be (except for context) either "he is" or "he has," but if the speaker draws it out, it will come out as "he has.'"
At the very MOST, the speaker may downplay the initial "h" (which often gets somewhat lost in rapid speech anyway) and say
"He 'as gone there many times."
There's no appropriate occasion for you to say "He is" when you mean "he has" -- even if you know DOZENS of the speakers I have just claimed do not exist!