It's hard to describe with all the in's and outs - but the main thing you do not want to happen is for backlash to be invoked at every step of the autofocus curve. You would be able to tell when that happens.
Some scopes, like sct's, have a preferred direction of focus - but others may not matter as much.
If you are using realtime temp. based focusing then yes you would also not want to have backlash compensation due to temperature change.
If there is a conflict then see if somehow you can change the direction of the numbers so it all goes from high to low.
Yes - it should be ok to go too big on backlash compensation. As long as the backlash is removed and everything is repeatable it should be ok.
Frank