If you can get them to do it, sure, go for it. I think that without evidence of a leak, you’ll have a hard time getting them to agree to pull the livewell just to check to confirm there isn’t a problem.
Were you noticing water leaking from under there? Is there anything, other than failed sealant, that would indicate to you that you have a problem with the plumbing? Because a leak under there isn’t necessarily going to cause the issue you had, although the sealant separation might make it more evident in that the water could escape.
Bottom line, if the only “evidence” of a water leak is that the sealant failed, I fail to see justification for pulling the livewell, which is pretty much what I think your dealer is going to tell you.