As a followup to this problem, just looked into the latest version of Omnitools, it now by default only whitelists oredict names containing: ore, dust, ingot. This should fix the exploits.
But if anyone is interested in an alternative, allow me to shamelessly plug this addon:
OreDupeFix. It is not exactly a replacement for the Forge Lexicon, but takes a different approach to solving the problem of duplicate items.
Instead of providing a means to convert between the same-yet-different item types, it attempts to unify all of the items before they are created: items in crafting recipes, furnace recipes, IC2 machine recipes, dungeon loot, etc. are all replaced with the ore type of your choosing (the default config uses RedPower ingots and Thermal Expansion dusts, but it can be changed in the config to your liking). Hope this helps someone.