They should work (or break) equally no matter if they are stored in ~/Documents/Test.alias or ~/Documents/Your Project.scriv/Files/Docs/UUID/content.alias. To the Mac these are just two different folders. If anything an alias should be a little more robust when stored within Scrivener, as we store the original path name when you create or import one, and if it detects the alias is broken, it will do a little local searching to try and discover the file around the original location, and “heal” it if it can. Most commonly this will fix cases where the you use Dropbox with different acount names.
As noted the alias itself is resiliant to changes in Finder, but there are limits. Copying the alias to another computer for example, will break it, even if the file is there somewhere.
So to really get to the bottom of this, we’d need to know a lot more about your workflow, and what it takes in a procedural sense, to get an alias from function to broken.