Agreed. It's rather poor design, really - clearly intended for a different era in which unique / untradeable items weren't nearly as common as they are now.

Still, I'd rather see this as part of a broader UI redesign. Clean up the layouts a bit if possible, and make response times snappier. Flatten the appearance to align it with the new launcher and generally modernize the experience. Implement that multi-select feature you mentioned, which would be a huge benefit for selling items to NPCs or desynthing en masse. Fix those weird scenarios like Triple Triad in which menus cannot be opened (all menus should be accessible at all times unless there's some database-related reason why they can't be, i.e. the Chocobo Saddlebag). Give us the ability to remove all confirmation prompts, not just when discarding unique / untradeable items (should be able to desynth or convert items without a prompt; shouldn't see a second prompt when declining the option to turn in additional Levequest items on the repeat quests; etc.). I'm sure there are any other number of things that can and should be modernized.

SE has spent a couple of expansions now working on the job abilities, so I think a similar effort oriented around the UI shouldn't be out of the question. So long as they continue to empower the player with their efforts - which they've really done a stellar job of so far, in all fairness - I see only upside to such an effort.