What are the pros and cons of adding flavor extracts (fruit, chocolate, what have you) at bottling time versus adding them to the secondary? Does it make a difference? Is there a trade-off between one versus the other?
Extracts can be added at either secondary or bottling to get the same results. I don't see any trade offs or benefits between them regarding the final beers flavor.
The pro at bottling time is to add a little at a time and sample the beer as you go to dial in the flavor. Once you have a set amount that works for your recipe, you can jsut add that amount all at once.
The only time you'd add an extract in secondary is because you need it to sit an age or condition a bit. But extracts don't really need that sort of development, so you're just better off adding at bottling. In the bucket with your priming agent, the rack the beer on top getting a good mix. No need to add the stuff at secondary ever, IMO.
Adding something like fruit introduces additional fermentable sugar to the process. If you do that at bottling time, you may run a risk of creating "bottle bombs". So the sources i've read suggest doing that in a secondary, with the same controls as for a primary fermentation (an airlock or something equivalent).