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From the same post you just quoted in it's entirety, and in answer to your "what if" question included deep within the quote, I re-quote :)

There are no "stringers" in your boat. It's just a fiberglass shell around foam. If there was water in the foam around those holes, your repair shop would have addressed the issue when they made the repair. This usually involves removing the wet foam and then replacing it with new foam, then closing the hole in the fiberglass.

The repair, done correctly by Boston Whaler recommended procedure for a hull breach of any kind, and I again re-quote:

involves removing the wet foam and then replacing it with new foam, then closing the hole in the fiberglass.

Again, if you or your repair shop did not notice wet foam when they made your repair, you did not get water in those 2 holes. Believe me, if that foam was wet, it would definitely not have gone unnoticed by the repairman. Even when simply filling the holes with any material that has been discussed in this thread, the repairman must have intimate contact with the surrounding foam. Some of the methods cited in this thread would absolutely require dry foam to hold.
If the trailer people accidentally drilled those holes, you had the repair done before you put that boat back in the water! It would have never even been exposed to water!

Don't be sick, sick, sick... Be happy, happy, happy that you have avoided a potentially serious issue by your own and your trailer shop's quick attention :)