@Anonymous ,
After much hair-pulling, I figured out how to view more routable layers in the footprint editor. I had the same use case as you - needing to define a custom PTH slot and have internal layer pads (not only does this let me connect traces to the pads on the internal layers, it keeps EAGLE from auto-pouring copper from other signals over the slot!). I also could have sworn seeing the option to edit internal layers in a footprint editor before, and this was in EAGLE 9.x.x.
Then, for some inexplicable reason, I noticed that one of my libraries had layers 1-3 and 14-16 available, but I was working on an eight layer board and needed layers 4 and 13 also. Since EAGLE files are in XML format, I decided to open up the .lbr file in a text editor.
Toward the top of the file, I saw these lines of code:
"<layers>
<layer number="1" name="Top" color="12" fill="1" visible="no" active="yes"/>
<layer number="2" name="Route2" color="1" fill="3" visible="no" active="yes"/>
<layer number="3" name="Route3" color="4" fill="3" visible="no" active="yes"/>
<layer number="4" name="Route4" color="1" fill="4" visible="yes" active="no"/>
[and so on]"
I made sure my library file was not open in EAGLE, then I changed the <layer> tags for 4 and 13 from 'active="no"' to 'active="yes" and then opened up the library, and sure enough, I was able to now define polygons in layers 4 and 13! The footprint works as expected. I also discovered that placing a PTH in the center of a polygon pour on a routable layer causes EAGLE to consider that polygon as part of that pad. Similar to arbitrary SMD shapes, but for PTH pads...only problem is now I have pads and drills in the middle of my slots, which end up getting exported to the Gerbers, annoying, and possibly confusing.
This is definitely a workaround Autodesk implementing arbitrary pad (PTH) shapes for PTH slots, which hopefully will happen soon.
Charlie