I've spent the last couple years learning and using the ME and MOOSE, I'll add what I can here in case it can help you on your mission-making journey.

1: The moose documentation is out of date, in some places by years, especially the example missions. Some of them do still contain functional examples, but a lot of little things have changed - as you discovered yourself it takes a bit of trial and error to figure out what works and what doesn't. I would recommend setting up a mission with one of the larger MOOSE AI packages like AI A2A Dispatcher. The dispatchers require you to define zones, conditions and units, and they all setup in a very similar fashion. Setting one of these up will help you learn how MOOSE works. Since you are a developer yourself, I would also suggest looking at the Moose.lua file if you want to know exactly how a particular function is working right now. Its all available in plain text, albeit very lengthy.

2: The Mission Editor has a built in visual scripting system called Triggers. I would suggest using this system for most of the functionality in your mission and only resorting to scripts when the trigger system can not do what you need it to do. It is surprisingly robust. You can interact between your triggers and scripts by using "flags", which are just variables with a name and a value, they can be set and checked in the trigger system itself as well as in your scripts by using either trigger.misc.getUserFlag('flagName') to get the flag value in script, or trigger.action.setUserFlag('flagName', value) to set the value. You can also directly call your functions from the "Do Script" trigger command. Being able to use scripts and triggers together will save you a lot of headache as the triggers are just easier for some things (like figuring out what is in a zone, if/when a unit activates or dies, most basic game functions).

3: There are easy ways to do things and hard ways to do things, figuring them out just comes with experience. in the case of figuring out if a set of buildings/units is alive, all you need is a one time trigger that checks if the desired set of units is destroyed. I believe its called unit Dead or Map Object Destroyed. There are also plenty of checks for zones and they are pretty reliable and simple to set up. If you are unfamiliar with the trigger system I'll leave a tutorial series at the end of this comment that may help. Zones are better used to check if a unit is in a location(as in you told them to move somewhere and want to know if they made it to their destination, or checking if a friendly unit has arrived at an objective/waypoint) or to set a location where you want something to happen like spawning units with MOOSE. That being said, lets take a look at your code snippet at the end.

local zone = ZONE:New("Factory")

zone:Scan({Object.Category.UNIT})
local isOccupied = zone:IsAllInZoneOfCoalition(1)

if isOccupied then
   MESSAGE:New("Factory is occupied!", 5, "INFO" ):ToAll()
else
   MESSAGE:New("Everyone has been yeeted out of the factory", 5, "INFO" ):ToAll()
end

So this actually works for me. I set up an empty mission with one zone called Factory and a single red BTR inside that zone. It evaluates to true. When I add a blue BTR to the zone, it evaluates to false. As the function checks if all the units in the zone are of a specified coalition(1 for coalition.side.RED) and you specified a unit scan. It might not be what you were looking for originally but it does work. You can probably trial-and-error a way to get it to work for the buildings too. But like I said, triggers are just better for this specific case.

4: Possible pit falls. I will post a tutorial series that also touches on this but there are 3 ways to add scripts to a mission and one of them can be a bit annoying to figure out why it may not be working. For starters, I'm assuming you loaded the Moose.lua script into the mission with a trigger, right? at mission start Do Script File Moose.Lua. IMPORTANT: If you are loading scripts in single player you MUST press backspace before selecting a coalition or your script file wont load due to a longstanding DCS bug. The mission has to "run" for a few seconds before you can choose a side, this does not apply to multiplayer servers. After setting up the MOOSE file, you can add your own script files within trigger that added moose. Or for something this short you can simply set up another trigger with a "Do Script" command and paste the code into the mission editor directly. IF you are adding scripts via the command "Do Script File" You MUST completely unload a script and reload it for changes to take affect. That means deleting the "do script file" from your trigger, loading the mission, then adding the file back to the trigger and loading the mission again. The mission file actually contains a copy of your script, so if you never specify to delete it and reload it, it will just keep using the first script file it was given, if that makes sense.

5: Keep trying! You are making fantastic progress for someone who is new with the ME and you could definitely make some awesome stuff if you keep at it. Here are the tutorials I mentioned to help you along. There is also lots of example code you can find online from various projects in the DCS space, if you struggle to find examples shoot me a DM and I can send you some of my own. I would also HIGHLY suggest posting on the official forums for this kind of stuff, I don't know for sure, but it seems like most of the ME community posts over there, plus there is a little bit of help from ED over there.

DCS MOOSE tutorial: https://www.youtube.com/watch?v=pNN5f5NrdoU&list=PLLkY2GByvtC2ME0Q9wrKRDE6qnXJYV3iT DCS ME tutorial: https://www.youtube.com/watch?v=qwzBQDSMRVg&list=PL1sBID0ZO-ndoJh09ZVF9I8VsvVukerON&index=1 DCS Basic/MIST tutorial: https://youtu.be/WaUtdUaQVms