I know of an explanation that accurately explains of the references to this point.
Start by looking at Hebrews 11. Specifically in verse 4 it says,
>4 By faith Abel offered unto God a more excellent sacrifice than Cain, by which he obtained witness that he was righteous, God testifying of his gifts: and by it he being dead yet speaketh.
Notice the underlined section. What this basically means is that even though Abel is dead, the witness of his actions "yet speaketh."
Now consider the last two verses of Malachi.
>5 Behold, I will send you Elijah the prophet before the coming of the great and dreadful day of the LORD:
>6 And he shall turn the heart of the fathers to the children, and the heart of the children to their fathers, lest I come and smite the earth with a curse.
Malachi also says this at the beginning of the last chapter, which then links to Mark 1 and the other places about John the Baptist:
Malachi 3:
>1 Behold, I will send my messenger, and he shall prepare the way before me:
So, what if the following: Just like how Abel "yet speaketh," despite being dead, we also see in John the Baptist, a voice in the wilderness, the voice of Elijah (that Malachi mentions) basically being repeated as John cries out those words "prepare the way of the Lord, make his paths straight" as Mark says in chapter 1:
>1 The beginning of the gospel of Jesus Christ, the Son of God;
>2 As it is written in the prophets, Behold, I send my messenger before thy face, which shall prepare thy way before thee.
>3 The voice of one crying in the wilderness, Prepare ye the way of the Lord, make his paths straight.
So then the explanation is that Elijah yet speaketh through the ministry of John the Baptist when he said those words, yet of course John the Baptist is not literally Elijah, hence his answer in John 1. Yet in a sense, Elijah returned in that moment when John spoke those words because they "belonged" to Elijah, as the prophet Malachi states and the Gospels note it as well. This would be the explanation of Jesus' statement in Matthew 17:11
>But I say unto you, That Elias is come already, and they knew him not, but have done unto him whatsoever they listed.