I sort of use the bucket method.
The area I live in has high nitrates, so I have a filter that I attach to the tap to deal with that. The only down side is that water flow has to be slow to ensure the nitrate is removed. I have several 25L containers, which I've measured and marked for 20L (easier for me to lift), and I add the water conditioner before filling with water. It takes around 10 minutes to fill to the 20L mark. I fill several containers before starting tank maintenance (to avoid getting distracted and flooding the house).
I have FX external filters on the larger tanks. I tend to run a long hose from the drain port, and water the garden whilst draining around 40% of the water. I then pooh hoover the substrate, which is much easier for me to do with a lower level of water. Using a shorter hose on the drain port, I put the other end of the hose into a bucket, and empty the containers of treated water into the bucket to be pumped into the tank.
I've never considered the issues of mixing the water conditioner previously, though I'm guessing that my current system on larger tanks should provide enough mixing to deal with any issues. I'm also lucky that my biggest tanks (river tank and axolotl tank) are both cold water, so I don't heat the water. I also use some RO in the river tank.
For my smaller tanks I have 10L water containers, and follow a similar system as described above, but also add some hot water after using the nitrate removal filters.
This has given me a lot to think about. I think my system for the larger tanks is ok as it usually takes a few hours to run the water, drain the tank, pooh hoover, and refill. It also involves a lot of water movement, and pouring treated water from the 25L containers into the bucket should ensure good mixing.
Slightly off topic of chlorine/chloramine, but also part of water changes, my tap water comes out at around pH7, but when left eventually settled as around 8.2-8.4. Can we throw pH fluctuations into the discussion as well?