Zach,
Your experience with built motors is exactly the opposite of mine. I would suggest your experience with built motors has been less than satisfying because your engine builders have not been up to snuff. I have an engine builder, that is also my tuner and my fabricator. There is also port and polish experience on staff, but that work is only done on the owner's cars. My built motors have never smoked, acted temperamentally, drank oil or did anything other than provide me driving bliss. I sold my built, 3L shortblock to a good friend and he's put more than 70K miles on it since 2004.
I didn't realize daily driving was the standard you were using. My black car is not daily driven, but it certainly could be. The HKS stroker comes with a billet crank, Carillo rods, coated HKS pistons, OEM oil squirters, an oil drive gear and the like. Assembled and maintained properly, there is absolutely no reason for the motor not to last virtually forever if driven in the same manner and making the same power as a stock block motor. But, no one builds a stroker to putt-putt around (not saying that you do). Guys build strokers, generally, to make big power. More power means more stress on all parts so, unless you are going to limit yourself to your stock block driving habits and power levels, a built motor, whether 3L or 3.4L and driven as God intended, is going to be less reliable than a stock block motor not routinely driven to its limits.
You've mentioned the 87 mm bore issue on several occasions, assuming this creates a reduction in liability. First, from my own personal experience, this is not the case and, second, many built 3L motors already have 87 mm pistons. I know I did, so my increase in displacement came solely from the increase in stroke. I may have a bit over 10,000 miles on my motor, but that is why I mentioned the more than 25 1000+ whp dyno runs, the bike racing and the dreaded SoCali bumper to bumper since, other than the bumper to bumper, it is not likely you subjected your OEM stock block to such stress (I could be wrong, but this is what I have gotten from your posts). It's my opinion that there only a few really good Supra engine builders around, notwithstanding the plethora of Supra shops. Finding a good engine builder is the same as finding a good doctor, lawyer, CPA and the like. The price is extremely steep if you fail in this key step. Best of luck with your decision.
Ken.