The evidence is behind the following episode of Mark:
At noon, darkness came over the whole land until three in the afternoon. 34 And at three in the afternoon Jesus cried out in a loud voice, “Eloi, Eloi, lema sabachthani?” (which means “My God, my God, why have you forsaken me?”).
35 When some of those standing near heard this, they said, “Listen, he’s calling Elijah.”
36 Someone ran, filled a sponge with wine vinegar, put it on a staff, and offered it to Jesus to drink. “Now leave him alone. Let’s see if Elijah comes to take him down,” he said.
37 With a loud cry, Jesus breathed his last.
35 When some of those standing near heard this, they said, “Listen, he’s calling Elijah.”
36 Someone ran, filled a sponge with wine vinegar, put it on a staff, and offered it to Jesus to drink. “Now leave him alone. Let’s see if Elijah comes to take him down,” he said.
37 With a loud cry, Jesus breathed his last.
(Mark 15:33-37)
Please apply the Hermeneutic of Suspect, here.
''Mark'' (apologist) was reacting against recent voices (and ''recent'' here means post-70!!!!) that claimed that Jesus was a seditious Jewish rebel who died in the role of the precursor of the Messiah. See also Mark 13:21.
Basically, according to these voices, the last words of the crucified precursor of the Messiah on the cross were:
''spirit of Elijah, spirit of Eliah, why have you forsaken me?''
So Mark is denying these embarrassing recent voices. It was not John the Baptist the Messiah of the Christians. John the Baptist, as Elijiah-redivivus, was only the mere precursor of the Christ. He was not the same Christ on the cross.
So there is the explanation of the why John the Baptist's memories were coalesced with the growing Jesus legend.
I would doubt even if John's death was a decapitation and not a crucifixion. In the latter case, then the Josephian episode was accordingly an interpolation meant to deny that John was the Christ (since John was not crucified).
But originally, before the 70, there was no link at all between Zealots à la John and the hallucinated apostles/visionaries of the celestial Christ.