Yes. In addition to mixing and exporting (rendering) to a single audio file (WAV file), VOCALOID6 features a multi-channel export function that you can use to export multiple tracks to separate audio files.
Select "Audio Mixdown" from "File" on the top menu.
However, other file formats (such as AIFF and MP3) are not supported. Note that the sampling frequency and quantization bit rate of the exported files are fixed at 44.1 kHz and 16 bits, respectively.