Well, I have to say that you are the only person I've ever heard give advice against doing 100% water changes for a betta in an uncycled container, so I wouldn't say that it's NEVER recommended. If you match the temp, use the same water source, and be sure to condition the water you really shouldn't have any problems. I'm not sure what the beneficial bacteria on the skin is that you mentioned. I've only heard of beneficial bacteria in relation to a cycled tank, and that bacteria resides in the filter, not on the fish.
I was having trouble with doing full water changes - until I got rid of the gravel. Even though I was changing everything, including the tank (spare tank, two thermometers, prepare spare, move fish, clean that tank, lather, rinse, repeat), I was having trouble. I finally got rid of the gravel, and stopped losing fish. I am not sure if the gravel was retaining bad bacteria, despite being thoroughly rinsed in hot tap water - or if even dry the tap water had something in it.
I'm now doing a full tank switch for one fish - she's reasonably placid and I use a small ladle to move her, not a net. The others I drain down with a plain tube suction down to just fish-high water, and then replace with water of the same temperature (I use bottled spring water - not going to even try to get the tap water working). Once every few weeks I remove the fish and drain the tank. Scrub it down with an algae sponge and aquarium salt; rinse with the bottled water; wipe down with paper towels. The decorations and heater are rinsed in the hot tap water, but then I also soak them for a while in a 'bath' of the spring water with NovAqua (gotta do something with the stuff - I use Prime in the actual tank water - as well as a bit of the aquarium salt)
The 6 I have now I've had ranging from 4 to 8 months. Given I was losing one a week for a while, this seems to be working for me.
dg