To do that, you'd need to either use a web browser with Java Script or use a container field for the bar of your bar chart.
Actually I figured out a workaround.
I created a repeating field with 100 repetitions. I placed it on a layout, oriented horizontally and showing all 100 values. In a script I set them all to "0" and then loop through the repetitions, setting the value to one then incrementing by 1 until I hit the percentage number and jump out of the loop. Using conditional formatting I set the background of the "1"s to a certain colour. Then I got even more fantastically clever and I used the conditional formatting to set the background colour to be green if the percentage is less than 33, orange if it's between 33 and 66, and red if it's more than 66.
It's not the most elegant hack in the world, but it does what I need it to.
I still cannot for the life of me figure out where there is such an absurd amount of space to the left of the chart created using the chart tool. Or why it appears to be leaving room for a second data set that isn't there.
What you describe is a limitation I have also seen with chart objects. It should be reported over in Report an Issue as a software bug. (I checked the Known Bugs List database and couldn't find a report on this like I thought had been added.)