A replica 386 would be impractically large - it's got around 275k transistors, compared to the 3.5k in the 6502. At the same scale as the MOnSter 6502, that'd be about a hundred square feet of PCB.

The number of layers isn't even remotely close to being a constraint. The real i386DX was manufactured on a process which only supported two metal layers, and a PCB version isn't subject to the same constraints as silicon.