Yes, you can file GC (PERM,I 140,I 485) without any issues.. PERM and I 140 have nothing to do with status .It is only at 485 stage where USCIS check applicant immigration status..

I think there is a provision for appeals(if out of status )for more than 6 months if the entry to US is inspected ( gone through immigration process in POE)..I've read some articles who have won cases( if inspected )in some circuit court.

I am not lawyer .. Please check with immigration lawyer..