Regarding what is covered in a boat that is four-years-old: the warranty statement (linked above) mentions three terms of length of coverage. There are items covered for one year. There are items covered for three years. There is the hull itself, which is covered for ten years. Since the question was in regard to a boat that was four-years-old, the only possible element of the warranty that would apply would be the ten-year section.
The ten-year-warranty seems to only cover "structural" defects in the hull which would render the boat unusable. I don't think a leaking in a caulk seam at the joint of the console to the deck due to shrinkage of the caulk would qualify as a structural defect, nor would it render the boat unusable. Here is an except from the warranty, and note it is identified as being the first element of the warranty:
Warranty Statement wrote:1. Ten-Year Structural Hull Limited Warranty: Any Structural Hull Defect in material or workmanship
which is reported within ten (10) years from the date of sale to the original retail owner will be repaired
or replaced at Boston Whaler’s sole discretion. The “Hull” shall mean the single fiberglass molded
shell and integral structural components. A Structural Hull Defect shall mean a substantial defect in the
Boat’s Hull which causes the boat to be unfit or unsafe for general use as a pleasure craft under normal
operating conditions
Note that any repair or replacement is "at Boston Whaler’s sole discretion." This is a another limitation in the warranty coverage. From what I know, in the past Boston Whaler has demonstrated good will in making repairs to structural defects that arose in the first ten years of a hulls normal operating conditions, and I don't believe they would attempt to avoid making a repair under warranty when such a repair seemed to be reasonably justified.
ASIDE: Thanks to PHIL T for digging up the link to the current warranty statement.