Ok, I can confirm that the latest dev version *seems* to work. I made a copy of my Infinity instance (Thanks MultiMC!), disabled TiCo and its addons, deleted dimlets.cfg. Sure enough, the dimlets in a chest I had placed in a world made specifically for this purpose were all scrambled. Then, I closed Minecraft, updated RFTools to the version in your link, and re-enabled TiCo, Tinker's Mechworks, ExtraTiC, and TiC Tooltips. When I went back into the world, the dimlets in the chest (all the digits and Liquid Short Mead, which was the last one listed in NEI) were all the same.
I did get a message when trying to load up the world that a bunch of RFTools shield-related blocks were missing. Should I have been worried about that?
I also noticed that the dimlets seemed to be listed in a weird order in NEI. The items' damage values, it seemed, were scrambled somehow, meaning that, for instance, 6258:486 was listed before 6258:481. It seems that NEI was sorting the items by some number other than the damage values listed in the tooltips. A very minor issue, if anything; just a little strange. And probably an artifact of exactly what you've done to fix the issues you've talked about.
Anyway, after that, I deleted dimlets.cfg AGAIN without also disabling TiCo and addons, which definitely should've scrambled the dimlets under the old system. But it didn't- I still had the same old digits and Short Mead dimlets. So it certainly seems to work.