What I believe you are seeing is the imprint from the ridges in the platen. All all Epson's you can look at the face of the platen and see a long row of raised bars, about 3/4" apart. The imprinting comes from the paper moving over those ridges, most times you can measure the gap between the marks on the paper and see it's the same.
I have not had this problem with Platine on my 9900, however I am still using Platine that is over 1 year old and I had heard from others it's been reformulated and thus not quite as thick. I can't address that as i have not purchased any in a while due to my current supply.
Every Epson I have owned does this to some degree, my 9880's being the worst, as they would leave the imprint in canvas and sometimes enough that it did not come out later during stretching. You can almost always see some of this on a glossy 250 weight, especially Epson's PPGP 250W, which has always surprised me. You can also sometimes see faint scratches on the back of the paper also left by these same ridges. I get the scratches on all paper's RC or Rag with my 9900.
The 9900 I have seems OK on my Platine, and Baryta 310 W. I know that Canon has reformatted Baryta as I have older versions that have a lot more glossy look to the paper where as their newer version is much more satin.
The vacuum, is basically suction. you can't turn it off on the 9900 or 9880, not sure on the 11880, but without any vacuum, you won't advance the paper. You have the option to reduce the suction when you load the paper, but as soon as you start the print, the suction comes back to the normal amount so, the decreased amount does not work while the print is running. When the print starts, you can hear the 9900 ramp the suction back to normal. If there is a way to keep it lower all the time I would love to know, i.e. a setting in service mode. There is nothing in the owners manual.
i went through several 9880's with Epson due to this issue, and finally worked out a deal to have to take my last 9880 back and let me pay for an upgrade to the 9900. I even had the repair tech on the phone with Epson to attempt to change the actual fans rams in my 9880's but it still left the marks.
I use Platine a lot and just ordered 4 rolls, and will test them on my 9900 to see if the newer versions of the paper leave the imprints like you are getting. The only way I know to totally remove these is in a dry mount process.
Paul