The guitar being played by the virtual version of Kurt Cobain in Guitar Hero 5 appears to be a hybrid of a Jagstang and the In Utero era Mustangs. It has the Jagstang body shape and the trimmings (pickguard and pickups) of the In Utero era Mustangs.
Of special note; the headstock shape is that of a Telecaster.
As speculated by forum members of Offsetguitars.com this could be due to possible copyright infringements; "Guitar Hero is sponsored by Gibson and Rockband by Fender".
Because the Cobain estate was involved in the creation of this character it is also a possibility that the headstock design was influenced by Kurt's favoring of Telecasters in 94 and/or later sketches by Kurt of the Jagstang which showed a smaller headstock.
Read Rolling Stone article on Cobain's cameo on the game here.
Actual game play video here.
Update: Krist and Dave have made a comment on the Kurt Cobain Guitar Hero Avatar.
Read statement here.