All toyota BOFs come from the factory like that, you probley just didn't notice it initially. It doesn't matter where you buy your toyota BOF, it will have missing spots of frame coating throughout every weld, and those spots will have light surface rust. Just go to any dealer, and look, every new 4runner, FJ, Sequoia, Tacoma, Tundra will have light surface rust spots on every weld.
They will either just stay like that, or get much worse depending on your environment, preventive maintenance, and normal maintenance. About a month ago, I finally had some time (took a couple of days during my vacation), and I applied 2 coats rust bullet automotive (grey) and 1 coat of their Black Coat (top coat) to every frame weld, and other rusted spot I could reach. All of the rust I encountered was light surface rust, but I wanted to protect it before it got any worse. Now I do feel alot better every time I am under there doing maintenance.
I chose Rust Bullet because, though similar to Por-15, reviews and long term tests have shown it to hold up better to Por-15, and be more forgiving then Por-15 when you don't follow every step/detail of the prep procedure.
For my prep, I just power washed the frame, and washed it down with automotive wash and an old mitt, then power washed again. I then scuffed any rust area I could find with either scotch bright pads, or 100 grit sand paper. I then rinsed, washed, and rinsed again. I used a towel and blower to dry the frame, and let it sit overnight to completely dry before I applied Rust Bullet.
I left the rust on a few components that are removable, like the LCAs, just so I could get an idea of how bad things would have gotten if I didn't Rust Bullet the frame. I don't care about easily removable parts rusting, it is having rust on major structural parts, that can't be removed, that drive me crazy!