Zizzo wrote:what sort of interface would you want for this?  I'm assuming that whether you want to auto-extract and keep a gem from an object isn't actually dependent on whether the gem is worth more than the object; would it depend on the object's tier?
My thought process (with no regard to add-on logic) is:  I want to have a stash of 
x gems per type per tier.  I tend to use lower tier gems for alchemist gems, and save higher tiers for the golem/imbuing.  (Where lower/higher tier is relative to whatever tier items are commonly dropping at my current level.)
If I have enough gems of a particular type/tier, I always want to transmo excess gems for maximum gold/fortress energy (whether it's the extracted gem or item).  If I'm still "collecting" a particular gem type/tier, I want to always keep extracted gems from "trash" items (i.e. items that are worth less than the extracted gem); and always transmo items for fortress energy when they're worth than if their gem were extracted.
Clearly this is a very specific use case to how I balance gems and amassing fortress energy, so I'm pleasantly surprised you're even inquiring. 
 
In terms of an add-on, that's way too complex.  I'd simplify it by having a gameplay option of simply "Auto-transmo extracted gems?" and make it true/false.  The add-on would use the existing "extract gems if worth more than the item" and follow the current tier setting, but always/never auto-transmo any extracted gems.
What I most use the add-on for is just determining whether an extracted gem is worth more than the item; I would be perfectly fine with never auto-transmo'ing extracted gems, and manually transmo'ing all gems myself.