I agree with you about some of the so called "Pros". As far as the average tinkerer goes, one example for the trials and tribulations of the LT/LS swap that can screw up a tune is the injection timing. Stock LS1 engines have no overlap, LT1's have varying degrees of overlap, if it isn't corrected you get a false rich condition when the engine is actually lean. You have the injectors spraying into an open intake valve while the exhaust valve is still open.
Most novice tuners trying to DIY, wouldn't know that and will be chasing their tail trying to get their VE corrected. This is just a single example, there are many other parameters that need to be addressed. My philosophy is to the best of my ability, to make the car hobby more enjoyable than frustrating for all involved. Sometimes the time and expense of these various upgrades is just not worth doing. Sensible, cost effective solutions on a case basis are usually the best way to proceed.