Dealers don't like to rebuild engines. Why? Many reasons. BTW, dealer techs ARE trained (if they attended the training) in engine repairs (internal and external). Kubota's training is pretty good but it's not perfect.
First, look at the amount of time it takes to do an overhaul. If a tech spends 40 hours on a rebuild at $120/hr, that labor in itself is $4800. Then lots and lots of parts. Including the dpf. Then sublet labor (machining, etc). I've actually done a few (very few) and if the engine was, say, $6500 brand new with a 1 year warranty, and the rebuild cost was $7000 with a 90 day warranty which do you think the customer is going to prefer? Can a tech do an overhaul in less than 40 hours? You'd think so, but honestly if you haven't done one (starts from the time they tow the tractor to the shop to the time the last wrench is put up and the floor swept up), that's probably going to be pretty close assuming they also have to R&R the engine. I've lost my backside a few times on engine overhauls. Secondly when you get into engines, there are a few things that can go wrong. For instance on some of them, let's say I pull the engine, completely tear it down, send it out for machining, then I reassemble with new parts. Then, after the customer gets it back it develops an oil leak at the back of the crank seal, now I have to pull the engine back off and repair the leak. And the customer obviously wants it done for FREE. They always do even if it's got 5 years' and 5000 hours' use on it. Dealer loses. Or if customer is not upset, but not happy, he'll tell his family members and friends that dealer rebuilt it but they had to pull the engine back off to repair a main leak, and now the dealer is the bad guy again. Or when they do get it back from the first repair, the owner says "they charged me $11,000 for an engine rebuild"....and their buddies standing around the campfire say "I had a new engine put in my truck for half that"....again, dealer is the bad guy. So dealers tend to take the path of least resistance for them AND for the consumer (usually).
Not to mention the cost of the tools. You can rack up a hundred grand in tools quickly, and they never really get paid for by doing repair jobs.
On outside rebuilders, their warranty pretty much sucks. They oft use component warranty and that's how they advertise it. Advertised "1 year warranty", and that 1 year applies to a particular component that carries the one year warranty, it might be a bolt or maybe a wire. They have to do it that way to compete, and to protect themselves.
Kubota engines are 1 year warranty if installed by an authorized dealer. That is the best option if a tractor needs an engine replacement.
Call some other dealers and ask them how much to rebuild it including removal and replacement. I bet the cost will be up close to or exceed the cost of a new engine with a good warranty. Last L01 I priced came out to shy of $17,000 to rebuild including replacement of the dpf and all labor. That was about 2 years ago. That one needed a crankshaft and block though. Needless to say I didn't get to do it; his insurance company actually totaled the tractor and he got a new one. Cost him $1000. If he had KTAC it would have been $250 and less headache.