This sort of discussion of tools and rooms and workshops always leads back to the two enternal voting suggestions for them. I like them both, and I think it adds a further and deeper dynamic development of fortress layouts. I have absolutely no problem with the game requiring specific furniture for specific workshop room qualities, and burrows being introduced is the first step to this.
Image you define a burrows in a non-square room, with the furniture lining the walls. You have the tables and chairs, cabinets, chests, armor racks, weapon racks, tool racks, tool shelves. You assign a few dwarves here (maybe a lot of dwarves), and you define some basic stockpile zones. Perhaps you have a piece of furniture like a cabinet or shelf or rack act as bin storage, allowing the stacking of 5-8 bins in one square. Tables and chairs accomodate the workers in their occupations and potentially rest. Define a one square drink and another one square food stockpile, and you have a place your workers can grab a snack from when they get hungry.
As for fisheries and fishercleaners workshops, perhaps you could equipment these with aquariums (if you have them), a pit for the fish full of water, a table for cleaning, a weapon rack to keep the fishing spears and cleaning knives, barrels to toss the processed meat into and perhaps to act as a sort of live well. perhaps another barrel or bin or some sort of refuse container could be used to have for bones and fish refuse.
Possibly you could turn fish chunks and animal chunks into chum, allowing for the baiting and angling of larger, more vicious and bloodthirsty sea creatures. If your dwarves could paddle out in a 3x3 boat, chum the waters, lay down lobster pots, troll with outstretched nets, fish off the side with rods and spears, and even potentially have to fight and lay down steel with the fearsome creatures of the depths in order to defend life and limb!
I don't see how keeping workshops as 3x3 modular place downs with the cost of a single unit of materials at the most basic, and a few materials at the most complicated is a good way to abstract the patterns and structures of work. Really take a look at it to see if the abstraction as a video gamey build unit similar to simcity is better, or having room based layouts similar to the sims is better, allowing your dwarfs to utilize the structures and furniture you sit down as the workshops and quarters better.
Try to distill the nostalgia for class DF design patterns out of your answers, and answer after that. Just because it might have been one way for a very long time, would going another way be an interesting switch up?