I received the Second-Row Interlocking Floor Liner for Christmas and just finished trimming and installing them.
After installing them I don't see much of an advantage for not cutting off the excess, as trimming them at the cut line still allows a few inches to slip under the front and end lip of the storage box. The storage box is formed with a bottom so if something in it should leak, it would be contained in the box and not get to the carpet. I suppose if you were hauling something bigger and/or dirty/greasy as the OP needed to do and required removal of the storage box then the added length would give your carpet a few more inches of added protection. But for me, if I need to haul something bigger and/or dirty, I'll put it in the cargo bed and tarp it if needed. I doubt I'll ever remove the storage box.
So far the only "Con's" I can see are:
They could have given better installation instructions, ie; They could have said you needed to slip them under the lip of the storage box. I had gotten it in my mind the reason for cutting the mat was so that cut lip of the mat would fit flush with the front of the storage box and I was ready to cut a few more inches off to make them fit that way. Good thing I stepped back and took a closer look and realized the mat lip needed to go under the storage box lip!
With the back edge of the mat under the lip of the storage box I don't think it will be as easy to remove for cleaning as I had hoped they would be, it's doable, but not real easy. But, they do look like they'll be fairly easy to clean with a damp cloth with them left in place.
All in all, I like the mats, they're very nice looking and a precise fit.