@Wolf little workaround with actual state of Freeter: use File Opener and point it to exe of your app 
even when you choose icon of that app from desktop, it will automaticaly get the exe path.
But it will stay as file icon. It would be nice to config icons and stuff, but i believe it will come one day 
Hello @Wolf , what you mean is ?
A) run two Freeters at once
B) open workflow in new window
C) one Freeter across more monitors?
from quick peak into code on github, I think:
A is probably not possible due to framework limitations
B should be doable, maybe with some limitations
and i hope it is not C
Note: I am not a developer of the app so take my words lightly
...
If you wanna play around you can try:
download source code and build "your" version of Freeter, named f.e. FreeterNotes. You should be able to install and run the original and yours, but each will have separated data/projects/workflows.
Exactly as @1kko wrote, you can define list of apps, or to be precise, paths to executable files of your apps, and then you can choose from that list in File Opener widget configuration. It overrules system default apps.
Example: If you have text file *.txt, Windows default app for txt is notepad.exe... lets say, you want to open notepad when you click that file outside Freeter, but you want to open VS Code, when you open it through Freeter - so you add VS Code (path to exe) to Freeter, and in File Opener widget config, you choose VS Code in last section "Open files in"... Or you can play with windows default apps for filetypes you want to open, so whenever you open it, via Freeter or not, you always have your app...
Not good example, but i hope you understand. There are more scenarios where it is actually usefull 
f.e. you work on webdesing, and you want to check your desing in all web browsers you have installed - you add all your broswers to Freeter and same amount of File Openers, every one with different "Open files in"
I am very sorry if I overexplained it too much, thats my disability from working on help-line when there was no remote desktop
