Hi Droseran I've found and confirmed that the Advanced Agriculture Compatibility Patches mod causes many modded workshops to disappear from the workshop menu for my maps since the update to 50.15 of dwarf fortress were as before your patch updated modded workshop additions were still able to show in the workshop menu.
If you'd like information like my mod list i'd be happy to help. The immediately identifiable things that this patch causes to disappear from the game are as follows.
Stoneworking Expanded menu and reactions
Wood Block Carpentry menu and reactions
Wood Processing Workshop mod, the workshop itself
Training Hall mod, the workshop itself
The above are the few immediate mods that I notice missing all the while ensuring that my load order has Advanced Agriculture, Advanced Orchards and Advanced Agriculture Compatibility Patches at the very bottom. If I disclude the Compatibility patch mod everything works as intended.

Thanks for the report, I'll look into this.

I can't get this behavior to occur.

My mod load order for testing:
Vanilla mods
Stoneworking Expanded
Wood Block Carpentry
Wood Processing Workshop
Training Hall
Advanced Agriculture
Advanced Agriculture Compatibility Patches
Advanced Orchards
Advanced Orchards Compatibility Patches

All modded workshops are showing in the build menu, and they have all of the correct menus and reactions when built (including the new menus and reaction in the Carpentry Workshop).

Do you have any other mods installed, and are you playing as the vanilla Dwarf (MOUNTAIN) entity? The reactions and buildings for the mods you listed are only added to the vanilla Dwarf civilization by their respective mods. The AA Compatibility Patch only adds reactions to other civilizations for the content in AA. If you're playing a modded civilization, they won't have access to the features in Stoneworking Expanded, the carpentry mods, and Training Hall.

My mod list is a quite large and is as follows minus the compatibility patch at the end, maybe it was because i needed it to be after Adv. Agri. but before Adv. Orch.?
Also yes I am playing as the vanilla dwarf entity.
"id": "vanilla_text",
"id": "vanilla_languages",
"id": "vanilla_descriptors",
"id": "vanilla_materials",
"id": "better_engravings_elaborate_design",
"id": "vanilla_environment",
"id": "vanilla_plants",
"id": "vanilla_items",
"id": "vanilla_buildings",
"id": "vanilla_bodies",
"id": "vanilla_creatures",
"id": "vanilla_entities",
"id": "vanilla_reactions",
"id": "vanilla_interactions",
"id": "vanilla_descriptors_graphics",
"id": "vanilla_plants_graphics",
"id": "vanilla_items_graphics",
"id": "vanilla_buildings_graphics",
"id": "vanilla_creatures_graphics",
"id": "vanilla_world_map",
"id": "vanilla_interface",
"id": "vanilla_music",
"id": "mineral_powders",
"id": "dwarven_chemistry",
"id": "dwarven_alchemy",
"id": "blast_powder",
"id": "clear_smoothing",
"id": "dark_depths",
"id": "alchemy_part_1",
"id": "broms_clean",
"id": "Burrows_Activation_Button",
"id": "broms_leather",
"id": "fantastic_trees",
"id": "beekeeping_buff",
"id": "Spellcrafts",
"id": "dwarven_therapist",
"id": "rose_beard_fix",
"id": "expanded_alcohol",
"id": "golder_gold",
"id": "no_attribute_skill_rust",
"id": "minecart_graphics_fix",
"id": "valuable_underground_trees",
"id": "cuter_cavern_moss",
"id": "metal_plants",
"id": "ironbark_tree",
"id": "glass_mechanisms",
"id": "Vanilla_Weapon_Overhaul",
"id": "Silk_Eggs",
"id": "glass_recycling",
"id": "slime_girls",
"id": "dwarf_arcaena",
"id": "SK_To_From_Arrows",
"id": "compressed metal bars",
"id": "real_alloys",
"id": "war_scythe_mod",
"id": "metal_plate_floor",
"id": "cr_mineral_fertilizer",
"id": "useful_kiln",
"id": "sling_shot_weapon_tum",
"id": "bunny_fortress",
"id": "flux_plants",
"id": "dwarven_steam_tanks",
"id": "recycle_clothes_and_armor",
"id": "ancient_races_dwarves_of_the_deep",
"id": "cr_recycle_cloth",
"id": "micro_dwarven_capes",
"id": "hivehorror_mod",
"id": "actually_red_redroot_dye",
"id": "ketaros_stonesvariations",
"id": "civilization_mod_pack",
"id": "more_bolts",
"id": "vetgolem",
"id": "military_uniforms",
"id": "dragon_size_fix",
"id": "invisible_filled_jugs_fix",
"id": "fb_ddd_steam",
"id": "niemst_colors",
"id": "caldfir_metallic",
"id": "plant_leather",
"id": "black_bronze_purple",
"id": "linmios_metals",
"id": "DW420_wd_icons",
"id": "fantastic_trees_civ_patch",
"id": "Kobolds_for_fort_mode",
"id": "caldfir_divine",
"id": "more_vanilla_creatures",
"id": "deon_crystallizard",
"id": "deon_peat",
"id": "embark_neighbors_extended",
"id": "niemst_water",
"id": "armed_dwarves",
"id": "niemst_grind_bones_and_shells_into_flux",
"id": "topples_bd_quarry",
"id": "training_hall",
"id": "bone_equipment",
"id": "jomt_carpentry",
"id": "woodblockcarpentry_eb",
"id": "woodshop_eb",
"id": "stoneworking expanded",
"id": "primitive_tools",
"id": "advanced_agriculture",
"id": "advanced_orchards",

I just tested my theory of the following load order at the end of my mod list,

Advance Agriculture
Advance Agriculture Compatibility Patch
Advanced Orchards

What I found is that it was my incorrect load order causing the issue, all workshops are displaying in the correct areas, apologies for wasting your time.

The load order:
Advance Agriculture
Advance Agriculture Compatibility Patch
Advanced Orchards
Advance Orchards Compatibility Patch

Should work just the same as the load order:
Advance Agriculture
Advanced Orchards
Advance Agriculture Compatibility Patch
Advance Orchards Compatibility Patch

I'll look into this, because the behavior you're reporting is not how it should be working.

Also, in your mod load order, the changes made by Valuable Underground Trees and Actually Red Redroot Dye are being overwritten by AA. If you want the higher values (VUT goes up to 5, AA only up to 3), load VUT after AA. The redroot dye mod is unneeded with AA, as they make the same changes and are incompatible with each other due to the use of CUT.

More Vanilla Creatures requires a patch mod to work with AA due to changes to the vanilla growths that the ents use: https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=3324629244

Ah thank you for further clarification and spotting incompatibilities, i'll make the suggested changes.