The two phrases you gave,
- The time has come for you to take over the company.
- It is time for you to take over the company.
have the same meaning, but the first is more poetic. It might be correct to say the first phase is an idiom. It's true that you have the present perfect of an active verb "to come" but the subject doing the action is "time". What? Time can't do anything!
After I first read your question I was thinking of a song I heard long ago which repeated the phrase "the time has come," and it turns out I was thinking of the 1987 song "Beds are Burning" by the Australian rock band Midnight Oil. But the search engine completion options reminded me of an example from a century earlier, which is from a poem that appears in the novel Through the Looking Glass by Lewis Carroll:
"The time has come," the Walrus said,
"To talk of many things:
Of shoes—and ships—and sealing-wax—
Of cabbages—-and kings—
And why the sea is boiling hot—
And whether pigs have wings."
Now at the risk of stating the obvious, a marine mammal of the species Odobenus rosmarus is speaking in this stanza. Oh, and the novel is about a 7-year-old girl called Alice who climbs up on the mantel above her fireplace where there is a mirror (that is, a "looking-glass") hanging on the wall. She finds to her surprise that she is able to step through the mirror, and she goes on to explore the world on the other side of the mirror.
In this case the poetic "metrical foot" contains two syllables with stress on the second. Each line has eight syllables which equals four feet, and for example in the first line the stress is on time, come, Wal-, and said.
Maybe the Walrus was not speaking grammatically correct and the first line should read,
"It is time," the Walrus said,
but that really doesn't work because now the line has the wrong number of syllables, and neither of the first two syllables is stressed. It completely mangles the poem.
So in this example, the Walrus must say "the time has come" for poetic reasons, not for grammatical reasons.
I don't know if Through the Looking Glass is the first place where "the time has come" was used to mean "it is time." But I can imagine that Australian rockers had heard of Lewis Carroll, or that other songwriters who have used the same phrase read the novel as children.