Now, enter the seasoned player with late 2013 mods on their Nth world who knows how to get ~100MJ/t fairly quickly, can setup one or a few diamond pipes with void pipes and chests fairly quickly, and is on a server. We now have a balance issue.
I would have to disagree with that conclusion. Being able to get resources quickly if you know exactly what to do with the various mods, is what I would call a complete non-issue. "Balance issues" in Minecraft, in my opinion, is what happens when modders become concerned about balance. I've been through quite a few worlds by now and getting a quarry up and running and watching everything working and the resources flowing in is still something I enjoy. I'd actually call it one of the absolute highlights of the whole tech progression.
Another vaguely relevant example to illustrate what I mean: I've been playing a Resonant Rise world recently - without MFR.
Fine, I thought, I'll give the other mods a chance for my tree farming needs. But it's not just that MFR is powerful and has ease of use compared to the other mods. It's also more fun to use (to me at least) as a direct consequence. Now I instead had to craft 60 identical blocks to get a tree farm. How did that make anything better in any way? And while I'm ranting, another example is Steve's Carts 2. It got "balanced", and as a consequence there are now balance issues.