I'm really not sure @PhatPhrank. Komodo doesn't do anything special. It just writes the file to disk as the user that you're logged in as. If it was doing something else I really think many many more people would be complaining about this issue. I would direct your focus outside of Komodo as I'm 90% sure Komodo is not the root cause here.
A couple things you should try:
- create a file in Komodo, check it's permissions in terminal, confirm that the correct user created it, stop and start Komodo, see if permissions changed
- Is there a process doing something with files on your disk?
- confirm you're not starting Komodo as super user or sudo
- I believe there is a program you can use to "watch" a file to see what processes touch it. Try tracking a file you've created from Komodo and see if anything (even Komodo) touches it when it's not supposed to and changes it's permissions.
- You might have a bad
umask which saves your files to disk with inappropriate default permissions. I know that's a thing on Linux. Maybe it's also on OSX since its a Unixs system under the hood.