The UI issue in the charts should be fixed by now - extreme values of scoring thresholds will affect scaling only to a limited extent. After this change, do you still feel that log scale is important for conveying the information?
By some parts of the dotted lines, do you mean that tooltips don't activate when you hover anywhere over the bar or the line chart? Or did you try hovering the space between them (which indeed doesn't currently have a tooltip)? These tooltips should list all accepted thresholds (were added a month ago, together with a 'show: max' option).
Regarding blacklisted thresholds, I've just added them back in order to validate the UI, but the roadmap is to treat brute-force solutions as rooted - for scoring and in the histograms. It will take a while to get there, so for now I guess they're here (despite their effect on the scores of nearby nonoptimal solutions).