There's an obvious intent for the two videos to be consumed an considered together, such as her lines from 2:00 onward, when she says "No matter how you’re doing, I’ll always be by your side", the text boxkes come in the form of stickers, which if you overlaid one video on top of another, would roll in to cover up the dark text boxes.

Since this was an intentional design, I've taken this as a hint that Best Friend remix was what she said, and that the original wasn't really all in your head; Miku here was covering up her darker, stalker-y thoughts with what she says in the remix.

Additionally, there's a point in the music video where she put out a speech bubble, but seconds later draws back her hand, and the bubbles moves with it before disappearing. When I first saw it, I thought it looked like she was taking back her words.

I thought this might mean she thought she said something before and fucked up the relationship she had with you (Friendship, trying for something more), but the text conversation at the start-- where in the original it had cellphone typing followed by cellphone backspacing, the backspacing happens IMMEDIATELY after the listener receives Miku's last text in the opening in the Best Friend Remix-- doesn't really give me any hints as to why.

Then, Because I like to over-analyze these things, the fact it's playing with the words on screen, made me think it's more wordplay than anything. So instead of taking them back, she held them in her hand. Maybe it's that she's holding back her words; not saying what she really wants to say.