Based on the user manuals, it appears the in camera low-level format does indeed overwrite the entire card. I think your confusion is from the two separate notes in the user manuals for newer Canon cameras that use SD cards. The other note about only the file management information being changed applies to a normal (non-low level) format. That notice has been in every Canon DSLR manual I've looked at for several years including those cameras that only have slots for CF cards.
6D Instruction Manual (p.54)
70D Instruction Manual (p.57)
Rebel T5i Instruction Manual (p.49)
Other Canon bodies that use SD cards have the same information in their respective Instruction Manuals.
Based on this specification, SD cards support the ability to overwrite the entire card quickly. CF cards are not capable of this.
Note: the above specification link no longer allows direct access. To read it, you should go to this page, click on the blue "Simplified Spec Archive" box below the chart, click on the "Download" button for version 4.10 at the top of the chart, and accept the disclaimer to view the PDF.