You could certainly do what you're describing.
What I'm gathering is that you've got the EARLY ATS setup that uses the factory air cleaner, it has an adapter that bolts to the intake manifold.
Like these pictured components:
You could acquire a Banks Manifold, and then the respective Banks Turbocharger (T3 flanged), verses the T4 Turbo the ATS (early) used. then plumb the intake and boost pressure to the turbo with the top hat.
I don't think it's a bad idea at all, I like the factory cleaner, well, if modified with the proper snorkel (like Dr. Lee's), you couldn't stack cleaners though, due to space limitations from hitting the hood tho.
I personally don't like the little Banks Air Box that gets used otherwise.
J
1982 C10 SCSWB 6.5TD, mods too extensive to list. (13.69 1/4 mile @94.6 MPH) RACE TRUCK
1982 C10 SCSWB 6.2NA, 2.73 700
1986 C10 SCLWB 6.2TD 3.73 700
1989 V20 SUB 6.2NA, 3.73 400
1994 G20 VAN 6.5NA, 3.42 60E
1994 K20LD ECSWB 6.5TD, 3.42 80E
1995 K20 SUB 6.5TD, Wrecked, ran into by stupid teen.
1995 C3500HD DRW 6.5TD, 12' Flatbed 5.13 80E
1995 C3500HD DRW 6.5TD, 18' Rollback Wrecker 4.63 80E
1994 C20HD ECLWB 6.5TD 3.73 80E Wifes Truck.
1995 C20LD ECSWB 6.5TD 3.73 80E
1995 K20LD SCLWB 6.5TD 3.73 80E
1996 K30 DRW 6.5TD 4.10 80E
1997 C10 Tahoe 2Door 2WD 5.7L to 6.5 Conversion Underway