When an item is duplicated from the base ambient loot chest to the actual container in which a PC finds it, it loses any variables (I assume) associated with it, meaning that it loses the summoning theme attached to it.

The implications of this is that if loot drops that is intended to summon monsters from a specific theme, it actually just reverts to the basic theme. This makes me sad.

It does? It shouldn't lose variables. Has this actually happened?

Well, if you mean like summoning scales and such items, scales atleast work and summon for example a II stone lizard.

Edit: also certain charm summons lvl I or was it II ghosts or so.

Just checked the script, and it should definitely preserve variables.

I found and used a Dog Whistle, and it summoned a Dire Rat. :( I've never felt so depressed.

Was it a fairly large rat? Collar it and call it a dog, problem solved.

Not even. -_- It's like a betrayal of summonry.

Issue identified and fixed.