I have done a lot of this kind of work with no major problems. The issues I’ve found are when the other apps you’re using interact with Obsidian in conflicting ways—e.g., inserting unfamiliar markdown syntax into a note, or adding characters to filenames that Obsidian doesn’t recognize.
A common mistake might be editing a wikilink in another app—if the app doesn’t recognize the change and rename the file/propagate it to other references to that file, your notes will get discordant.
But, again, in general, it works really well!