This is an excellent visualization of the significant performance improvements made from Beta 3 to 4. Thank you for sharing!
You are correct that thresholds have been added for index fragmentation. While AppInsight for SQL can leverage the new Baseline Calculator, it does not make sense for index fragmentation since it's a very well understood metric. The default thresholds are greater than 80% fragmentation = warning, and greater than 90% = critical. You can either chose to rebuild these indexes so they aren't as fragmented, or you can adjust or remove the thresholds entirely. This can be done for all SQL instances, each SQL instance as a whole, or even on a database by database basis.