Wasn't sure from the documentation whether this was supported. For instance, I'm building a pack with Binnie's Mods, and I want to disable his Brewery/Distillery combo and instead have players manually age their booze simply by letting Food Funk decay it. As an example, it would require being able to rot:

binniecore:glass {Fluid:{FluidName:"binnie.juice.apple",Amount:1000}}

Into:

binniecore:glass {Fluid:{FluidName:"binnie.brandy.apple",Amount:1000}}

Is this functionality supported? I couldn't quite tell, from the wiki. And if it's not yet supported, is it something you're considering?

Specifying NBT names and values in the rot ids is not currently supported. I'll look into it.

Do you know of any open-source mod that already supports specifying NBT tags and values in item specifiers? Finding code that already parses and checks for matching would make it easier to implement.

I believe these mods do so:

Modular Machinery (can define custom NBT for item inputs/outputs via the machine JSONs) - https://github.com/HellFirePvP/ModularMachinery
Villager Trade Tables - https://github.com/crazysnailboy/VillagerTrades/wiki/Adding-Trades#items-with-nbt-data

But those both use JSON instead of the simple config file. I'm still looking to see if any of the ones I'm familiar with use config.

I would also like to see support for NBT tags for preservation entities, as Immersive Railroading identifies specific rolling stock entities using them.

IR is open source if you are interested in looking at the code:
https://github.com/cam72cam/ImmersiveRailroading