Does Line Honing change the crankshaft's centerline?

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."

His question was
"Does Line Honing change the crankshaft's centerline?"

It's already been answered. He doesn't need a shorter timing set if the job is done right.