There’s still not enough details being provided to make much of a guess as to what the problem actually is but based on the comment about putting oil in it and a continuous rattling I can only theorize that it’s a rod bearing hammering away.
As to the 2-3k dollar cost and the question about why people don’t fix them anymore it’s a simple matter of economics most of the time.
By the time a shop figures book flat rate, procures all of the parts to do the overhaul with, and has all of the necessary machine shop work done (crank turning, cylinder boring, block vatting, head surfacing and/or valve work, etc, etc,) it’s more cost effective to go with a used engine or a remanufactured one.
A reman facility is an assembly line process and due to the business model they’re able to not only do the labor cheaper but are able to purchase their parts in bulk and get them cheaper.
No matter, I don’t see 16 hours of labor just to go poking and guessing. Jeez, run a compression check, drop the pan if need be, remove a valve cover, and at least attempt to narrow it down a bit before disassembling the entire engine; which should not require 16 hours of labor even for that.