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Vanishingly low with blood and bodily fluid transmissible diseases. Contact transmissible diseases like HPV and herpes are the main concern, but those aren't mentioned until later in the article, nor are transmission rates compared to the other types, so I'm skeptical that those alone don't merit extra precautions. Speaking of,

[toilet paper is] made of porous materials, so they cannot stop germs from seeping through and touching your genitals.

Seeping implies moisture, so yeah if there's a HPV contaminated drop of water on the seat, that'll wick right through to your ass cheek when you sit down on it. The obvious response being to give the seat a once-over with a wad of TP first to dry off any drops, then build that TP bird's nest around the seat. Pathogens can move on their own to some extent, but without a vehicle to push them through the TP (like a drop of water) the thickness of the TP relative to a single bacterium or virus would make that journey akin to hiking through miles of forest (*don't take that too literal, but any math gurus here, feel free to crunch the numbers!!), and in the few minutes it takes to shit, the feasibility of that journey being completed strikes me as fairly low. And even if some do make it through, you're still getting a lower pathogenic load than if you just raw-dog the thing.

The data and conclusions drawn in the article are unconvincing. Further investigation required; until then I'm personally going to continue to play it safe with the bird's nest routine. Also throw a wad into the bowl before dropping logs, as that'll prevent splashing.

Speaking as a surgical tech, I've helped cut condyloma off enough ass cheeks to develop a healthy paranoia to strange environments made to interact with my own ass cheeks. TP is cheap and painless. Surgery is not.