This is a massive blow, I spent ages setting up a brew specifically to have it in a kit (run a command) the command works in-game but as soon as you try and do it from console, NOPE! denied. what gives, this means no other plugin can give a player a brew???

Well, you might have problems with uniforming your brews, that why you can't give yourself a brew, but you can give it in kit. Every brew has it own item id(potion 3b for example), to become all your potions have same item is you must lead the amount of ingredients, sealing and brewing time and the quality of the brew. If these four indicators be the same, item id of all the brews will be the same too. Also read this for more info - #347 Good luck!

Ah well you need the permission brewery.cmd.create for that command. I don't know if it is even possible to give permissions to the console? And I didn't know the console does not just have all permissions??

For some reason when I tried it from the console it didn't work, but when I have it in an Essentials kit to run the command it works.
So it does work how I wanted it to work, but what is weird is not being able to do it from the console.