outboard dxf
It is very doubtful that the fab will be able to load or use your HFSS file. You should make a text document to describe exactly what you want them to make for you. For example:
1. This is a two layer board with finished thickness = 1.575mm
2. Copper thickness = (.5oz, 1oz, 2oz, etc.) on both layers
3. Final copper finish is to be (bare copper, tin, silver, SOBC, OSP, ENIG, etc.)
4. Material to be used is Rogers RT/duroid 5880
5. Please route out board to same size as bottom copper area, OR Please route out board with copper centered on Xmm by Ymm board, OR please route board with final size Xmm by Ymm with area described by Gerber files centered on edge of Y dimension (draw a picture if you can't make a Gerber file for the board outline).
6. ...
In other words, you put on paper the exact description of what you want the fab to make for you.
Yes, the Gerber files show the bottom copper plane even with the end of the trace on the top layer. You should give your Gerber files an extension of .GBR to avoid confusion at the fab. They are probably accustomed to seeing Gerber file extensions beginning with "G". There are other Gerber file extensions, but those are the most common. (Top_1.GBR, and Bottom_1.GBR)