Couple possible options. I doubt it's Vocaloid software proper, it sounds like an older sort of vocal synthesis program, less precise/polished than vocaloid. Could be a straight-up vocoder, with AG singing into a mic while manipulating the pitch and vibrato of a synthesizer patch. The sound seems most similar to the Ondes Martinot, which you may recognize from the title track on Radiohead's album Kid A.
cf. also AG's Heaven remix (the parts that aren't GFOTY/Spinee obviously), definitely a similar technique at work there