The 0.6 content patch will introduce a way to upgrade the max attribute rank to 20 but for now the plan is that Nemesis item drops will still be able to go beyond that. Currently the idea with Nemesis items is that they should be a fun bonus if you get lucky but are in no way required to complete the games content.
Regarding the Auto Scrap settings currently each individual item type (Default, Gems, Tools, etc.) is active at the same time, the drop down menu simply changes which item type you are currently configuring. Are you asking for a new drop down for "All Items" that will be run before each individual item type?