Slic3r under extrusion
It looks like you overtune it. I think it's because top layer of hollow object doesn't have any support (which is obvious) but because of that the filament is not oblate that's why it looks like underextruded.

If you really need hollow object then set number of top layers to 3..5 then check if it helps. I know it's not really what you expect but IMO this could help here. (I usually set 2 bottom layers and 3 top and it's quite enought.) You can also experiment with speed of top leyer. I would say the faster the better in this issue as the the first top layer should be as flat as possible then next top layer will have better support. And of course cooling should be set to max (as for the bridges).

Here is an explanation why you get underextrusion. 


A is wall (perimeter) B is (ceiling) top layer. 

Empty outlines are what you expect but filled shapes are what you really get. Differences are of course slightly smaller but it's to clearly explain the issue

Please also check Printer Settings > Advanced > Top solid infill.