It should be completely flush.
Now, clean all rust, paint, and grime out of the pulley in the area where the magnet fits. This pulley already has a new bearing or else I would change that too!
Put grease in the bearing bore and on the compressor neck. Tap it on the compressor and install snap ring. If it is tight, tap carefully on the bearing INNER race with a brass punch.
Clean and inspect the clutch hub. This is for a V5. You can tell by the triangle-shaped counterweight. The other compressors have a non-counter-weighted hub.
Mount the hub installer. NEVER drive hub on with hammer, it will destroy the compressor. Drive it about half way and then take the installer tool off. Inspect to make sure the key is in place. If the key falls out and gets trapped under the hub, it will destroy the new shaft seal, and possibly the housing.
Press the hub on with installer, until there is about a paper's width of gap.