You are 100% correct
2002 420 passage - same problem but three leaks all from the hull deck joint.
I removed the toe rail by removing the 50 screws holding it on. That immediately revealed the problem of very poor installation. The screws were too long and they had not been tapped and drilled, just power drilled at the wrong angle so had split the hull and deck lips. Because the screws were too long the ones at an angle had then made a hole in the hull. It took me three weeks to clean up this mess!
It is the hull deck joint. On my 49 this was a big problem, and ruined the wood in the fwd cabin.
Hunter sent a factory pro to my boat to repair the damage. Excellent service.
There are no shortcuts to repair this.
Toe rail must come off.
Keep track of which screws went where. As you remove them, duct tape them to the hull right where they came out.
You will find screws that are too long, too short, bent, etc.
You must clean up each hole, dig out bad sealant, inject new, and re-attach with brand new screws . Make sure the screws are not too long.
You don't want them going through the back of the hull deck joint.
Hope this helos