That 'caulk' job is a mess, no offense.
The flanges and screws should be bedded in sealant, not buried. The first plate seats into the flange and all that goop is just in the way. It's not causing your leak at least. This is how mine looked before teardown....
Attachment 18666
The flange curls into the exhaust tube and overlaps the pipe. Whether it's an inch or 4 inches up it's an area that needs sealant. 3m 4200 is perfect for this application but there are other sealants approved for below the waterline.
New sealant over old won't work well. Pull it all apart and clean it up. You'll see why the pipes need sealant, too.