My 40 has never had a floor mat, but speaking from experience on my Mazda 3, I have worn through two carpet top, rubber bottomed, OEM Mazda floor mats where my heel pivots between the gas and brake pedals. I'm well on my way through the rubber weathertech mat I replaced the OEM mat with. Because of this, my vote is for thicker material. That said, the pedals in the truck are higher so I don't pivot on the floor as much - maybe a non-issue??
As for logo - I also have no idea where the logo is, nor do I care about it. I mostly want a nice, formed mat to fit the floor and trans-tunnel and provide some protection from the exhaust heat. I'm with @kruisinkid on this one. I'm pretty set on black, but I think I'd buy a thick black mat for ~$400 or a thin one for ~$300. This is right in line with what we would all have been spending buying an OEM mat, and, let's be serious - in the grand scheme of a FJ40 restoration - what's another $400. I've never seen a single one of your products up close but that said, all reviews are positive, they look great in pictures, and I'm fully convinced I'd be getting a high-quality product.
I will go so far as to say that $700-$800 as @Bambi Girl would absolutely price me out. Totally open-minded about this, and appreciative, but no way do I have "Bambi" level disposable income!