Story mode maps in other modes
So let's say that hypothetically the bingo battle and mission mode stages are not enough for you, you need more space for your custom level, different enviroments and unique layouts. Okay then, your best bet so far would be Story Mode stages, here's how to use them in mission mode.
Making a graphic pack, getting the files and editing them
To begin you will need to create a graphic pack. To do that, create a folder, for the example we will be creating a folder named "Pikmin3_PikminAreNeat", inside the folder create a folder named "content" and a text file named "rules", you can either create one yourself or copy from another hack. After both are created go inside of the "content" folder, inside create a folder named "CMCmn", there create 2 folders, "system" and "generator", inside of the system folder make another folder named "mission_set", then go to the game files, go to CMCmn/system/mission_set, then find a miset file you wish to edit, for this example we will be using miset_mis1_poko (Which is mission settings for Tropical Forest Collect Treasure stage), copy the file and paste it in the "mission_set" folder we created in our graphic pack, then open Switch Toolbox and open miset_mis1_poko we copied earlier in Switch Toolbox, export the "mis1_poko.txt" file to any desired loaction, open the exported file and find a line "MapName", in our example we would want to use Tropical Wilds so we are going to replace the "mis1" that is found below "MapName" line to "mapA". After that save the .txt file and return to Switch Toolbox, there right click the "mis1_poko.txt" file and select the option "Replace Raw Data", in the new window select the edited version of the file. Then save by pressing Ctrl + S. Now go back to the CMCmn folder, open the folder "generator" we created earlier, there create a folder named mapA. Then go to game files, go to CMCmn/generator/mapA, open the "single.szs in Switch Toolbox, there export the "path.txt" file to any desired location. Then go back to CMCmn/generator folder in the game files, open any "misX" (X stands for any number) and copy "poko.szs", paste it into the CMCmn/generator/mapA we created in our graphic pack. Open it in Switch Toolbox and select "path.txt", right click it, in the new window select the "path.txt" file we copied earlier from mapA. After replacing save the "poko.szs" by pressing Ctrl + S. After that open the Pikmin Generaotr Editor for Pikmin 3. After opening it select "File" option, click "Load", select the "poko.szs" file in our "mapA" folder in the graphic pack. After that in the new window you can select 1, defualt or plant, you will need to wipe out all of these files, so open let's say 1 and delete every object, repeat for default and plant. After that select "Geometry", select "Load BJMP", in the new window go to game files, CMCmn/map, there select mapA_text, now you should see geometry load in the Gen editor. After that select "Misc", and select "3D View". Now you can edit the level.
Setting stuff up
Now that you have (Atleast i assume so) made a level, save it by pressing Ctrl + S, after that close the Gen Editor and go to the root directory containing the "Pikmin3_PikminAreNeat" graphic pack that we made earlier. Copy the graphic pack folder and go to your cemu directory, there go to "graphicPacks" and there go to "downloadedGraphicPacks", inside paste the graphic pack that we have created. Open Cemu and select "Options", select "Graphic Packs", double click "Pikmin 3", double click "Mods" and tick the box next to the graphic pack that we have created. Now close the window and open "Pikmin 3". Finally in-game go to Tropical Forest stage in Collect Treasure and play it, if you have done everything correctly you should have spawned in Tropical Wilds rather than in Tropical Forest. This means that it worked and you can succesfully follow a guide and also use Stages from Story Mode in Mission Mode.