Given I wash my film in the tanks (usually put through at least 10 batches of fresh water per film), there is no chance of contamination. It would be the same as you are subjected to wen you clean your tank after finishing processing, regardless of the process regime.

I, too, have the sink on the "wrong" side of the tank; however, this has never been an issue for dumping chemicals. The tank's mouth is always higher than the bottom of the hose when lifted, so it is easy to capture the stop-bath/fixer when they've finished their work. I'm not sure why you cannot do this? The only issue for me comes when I want to empty the tempered bath water where I need to turn the processor around to drain it. But, again, it would be easy to capture this in a bucket placed under the hose if I could be bothered…

You physically might feel that you have more control without the lift; however, I feel that the introduction of chemicals via the lift (especially the Developer) is a much better way than to have to pour it in to an upright tank. As the machine is agitating as I do it, I feel that the initial chemical contact with the film is both controlled and repeatable. I have never had an issue with banding etc. from introduction of the developer (but I do prewash, something I feel is necessary for good negs in Jobo).

Just my way of working. YMMV.