What's the evidence that the colors were added later?

[Bernd]

the paint job has the appearance of someone attempting to do something they don't quite master.

To me, the entire manuscript has this vibe.

So this would mean it is very unlikely the VM was painted during creation while still in loose sheets.
And that when it was bound and painted, it is likely the ability to make sense of it (implying there was any) was already lost.
Still 15th century is a bit vague. If the VM was created around 1420 that would still leave 1-2 generations until the binding.

I am looking forward to the recording of Lisa's lecture.