Having to mark every item for encrusting would be a hassle, and to me a regression gameplay-wise.
In the stocks screen you can mark and entire category at once. Just as now you can mark, say, all statues for melting or dumping with one key press.
Unless you are AFK mass-manufacturing and have a backstock of hundreds of gems I don't see how it is a big deal to mark things in the stocks screen. It's far less of a hassle than, say, the caravan trading screen.
In a pinch, there is currently a DFhack script that marks everything that gets put in a selected stockpile for melting automatically.
As it stands right now, if I want to stud one masterwork sword with a particular gem it's a massive pain. Or if I want to sew an image onto only superior+ emerald cloaks and hoods. Or if I want to stud all copper barrels with zinc bands. It either requires messing with the settings of stockpiles, or making a dozen Jeweler's shops with different linked stockpiles.
Or just do what we do now and just say "encrust stuff" and just let the dwarves grab whatever random junk they find and encrust it, often multiple times. Often bypassing objects you want decorated to go grab something else. Stud'em all and let Armok sort it out!
Let's do the example of studding copper barrels with zinc bands. Metalsmith's forge produces the barrels. All furniture stock piles need to be set to either disallow barrels or disallow copper items. Need to have a copper barrel stockpile and a zinc bar stockpile linked to a metalsmiths shop that has non-decoration labors disallowed. The zinc bar stockpile needs to be set to take from your main metal bar stockpile, because you need to make the bars available to the decorator without making the rest of your bars unavailable to other workers. Need to have an output stockpile allowing copper barrels linked to the workshop. And don't forget to set the output stockpile to 'take only from links' otherwise it will quickly fill up with undecorated copper barrels. Sometimes you have to unlink and then relink everything to get it to work. Also set the max bins in each stockpile to zero otherwise the decorator might now see the zinc bars inside the bin, as bins are buggy lately.
Then, if you want to stud something different you have to change the settings on all the stockpiles and make sure the workshop has had all the items in it hauled away. Or just build another workshop with another set of linked stockpiles and alter the settings on you main stockpiles again.
It would be nice to be able to go to stocks, move the cursor over the copper barrels, hit 'e' (or something) to flag them for decoration. Then set a job to stud with zinc bands on repeat. It will then do so until it says the job was canceled because no item was marked for decoration.