I guess this is a feature request.
First, background: In SR4's Chummer, it automatically locked you out of taking more than 35 points in neg qualities. Take 2x 20pt negative qualities and it throws an error dialog. In the House Rules tab of the options, there was an option to exceed the cap and avoid the error. If you selected that option, it enabled a second option to limit the points.
Currently, in Chummer 5, you can take negative qualities over your cap. (25 standard, 35 for prime runner). It will give you that extra karma to spend. The options from the previous version would be nice to have. It's not a high priority, obviously, as Chummer 5 has that handy negative qualities calculator. Anyone paying attention during character creation should catch it.
-Ariketh