As long as I am talking about polygons:
Here is the polygon. In this mode you can see through it.
Note I plowed though other polygon. I also went out to the edge of the board.
Now I pushed the RATSNEST button.
Note the copper does not go to the edge of the board and the other polygon cuts into this polygon.
NOW THE REAL QUESTION: How do you get back to the "clear" looking polygon? You might need to see through the polygon to rout traces.
ANSWER: I don't know how. There must be a easy way. I pick up a side or corner of the polygon and move it a small amount and then move it back. Any change will cause it to go clear.
This is what it looks like with THERMALS turned on. I do not do this. I am trying to get the heat from these parts to travel into the copper and be carried away. With the way I solder the parts the thermals do not help.
In some cases you want thermals on for all the little parts but you do not want thermals for the hot transistors and ICs.
Make a polygon with thermals on for the entire area or board. Then make small polygons (the size of the IC or transistor) with the thermal turned off. It is OK to have polygons on top of polygons. By stacking polygons you can have small areas with different effects. (thermals, clearance, line widths, etc)