I've been using the Dexter system since they came out with it, without a single issue, ever. If you follow the very simple directions there's a very good chance you won't have an issue either.
As far as the people that have had issues on another (RV) forum, that's kind of like saying you can expect a blown tire. You see a lot of complaints about those too. People complain when "stuff happens". The people without issues are generally silent. I think a lot of times it comes down to the fact you can't fix stupid.....
Bottom line, Dexter axle has an OUTSTANDING reputation. That's why you find them under so many rigs. If they design, test, and produce a system that been in use as long as this one has, and are STILL using it, I think it safe to say it's a trustworthy system.
When you add something like the Buddy Bearing system to Dexter's system, you are complicating the issue. To answer your question, if you're going to run the Buddy Bearings, there's no need to mess with the zerks installed in the axle. Just forget they are there, and use the Buddy Bearings as designed.