When a yo-yo is high-walled the face of the yo-yo is cut back resulting in more surface area of the yo-yo touching the string when it tilts; and a thinner profile. Both of these things are good traits for a freehand yo-yo and any other long spinning style. Also, a higher wall makes for cleaner string rejections, whereas the hard edge inside the gap will force the string out more directly.
High-walling is fairly easy to do on a Duncan yo-yo, but very difficult to do on any yo-yo with an integrated bearing seat, for example the YoYoJam Hitman. This is due to when you shave the face of the yo-yo down you need to lower the bearing seat as well. That is vary easy to do on a Duncan yo-yo because all you have to do is put in thinner spacers of sand the back of your spacers down. On a YoYoJam yo-yo or any other yo-yo that has the bearing seat built in you have to completely re-machine the bearing seat.
After YoYoFactory made the '06 888 they produced a small run of high-walled 888s. These were a big hit so YoYoFactory made high-walling standard on all of their '07 888s and Skylines.
In this picture you can clearly see how a yo-yo would look before (on the left) and after (on the right) being high-walled.
Oh look, a yoyowiki article that I wrote is being pasted verbatim onto the yoyoexpert forum along with my pictures for no particular reason.
Notice the raw aluminum face on the yo-yo pictured in that thread. That was one of the highwall test yo-yos that came factory modded by YoYoFactory and were sold as a small batch on yoyonation. It was not until the 2008 model that the highwall was a standard design feature. You would have known this if you actually read the thread that you linked to.