I am not a mechanic but somethings sounds "not right" I believe the "top end" refers to the head with the valves, etc. So, if the damage is to the pistons and connecting rods a top end rebuild will not address that. Either way, I'm betting you can get a working engine in your boat for much less either by finding a used engine or by getting a second opinion on the repair or partially doing the work yourself.
for the record..... top end includes pistons, rings and head
the bottom end is rods and crank...
if the engine needs to be taken down for any reason, the valves should always be inspected and new stem seals installed at a minimum...
other top end work usually includes new rings, and sometimes new pistons. if new pistons are needed, the cylinders need to be closely checked to see if the cylinders need machine work done... if all is good, then a good inspection of the rod and main bearings to see their condition. if they still look good, put it all back together and run it. if there is any noticeable wear on the bearings, replace the rod and main bearings..
when the bottom end is the problem, there is usually more expense involved, as a "problem" there almost always requires machine work and sometimes a new crank... and when this is needed, a top end rebuild only makes sense at this time.
a rebuilt engine will have all components checked and replaced as needed... a "freshened" engine will have the valves lapped/ground, new rings on the old pistons, and possibly new lower bearings installed.
many owners can easily do their own rebuild if they get to it before there is a problem. if they are familiar with the engine and it is a good working engine with high hours, it may be only a matter of new rings, new lower bearings and a head job to "freshen" the engine.
but when the weak engine gets ran until the engine starts making knocking noises, screeching noises, misfiring, overheating or extreme smoke, then it has just gotten about twice as expensive as it will undoubtedly need machine work done.. a full rebuild.
and of course, not to be overlooked are the peripherals such as the water pump, oil pump, injectors or carb/distributor, hoses.... and equally as important as the rebuilt engine is to make sure the exhaust is in excellent condition, because a bad exhaust doesnt care how much money and time you put into the engine, the bad exhaust will secretly take it out while it sets in your driveway after the test run.
when a mechanic is hired to rebuild an engine, or if a core engine has been purchased to be rebuilt, and the person doing the work knows nothing about its history, the engine needs to be torn down completely. all components need to be gone thru, cleaned and tolerances checked to insure the components are in usable condition,with all machine work done... and then build the engine back accordingly... this takes more time than a basic freshening