Does Line Honing change the crankshaft's centerline?

.003 -.005 off caps.

To answer your question:

They sell timing chains that are slighty shorter to compensate for the material being removed.

ROLLMASTER CS5150 – Timing Chain Chrysler Big Block 361/440 PRE/EFI Gold Series with torrington bearing & nitrided sprockets, 9 keyway crank sprocket, 3 bolt cam sprocket – Bill Mitchell Products

"Line Bore Kits available in .002″, .005″, .008″ and .010″. When ordering Line Bore Kits mark order with LB2, LB5, LB8, LB10 after the part number."