I think it makes sense to keep the project name separate. Some people will want to set them separately. For example you might have "My game (variant 1).c3p" and "My game (variant 2).c3p" for testing or experimentation purposes, and you want both to have the project name "My game". If the filename automatically sets the project name, it makes it impossible to do that - the file system will prevent you having two projects with the same name, because you can't have two files with the same name.
Thanks for the personal reply Ashley, I really appreciate it coming from the founder, and it's nice to meet you. I think the negatives considerably outweigh the positives. It makes file management very difficult. I can't think of other sophisticated software (which Construct certainly is) that operates this way. It should be an option in any case. Let the user decide if they would like to work in a more traditional fashion. Any time we make creative projects, be it in Premiere or InDesign or Reason, the file name is the project. It's natural and normal and efficient and logical.
I have hundreds of js files that I create and manage in VS Code, all declarations for content for educational games. I can't imagine if each of them had a separate name for the "project" and the "file," and then I also couldn't see the file name anywhere. It would be a nightmare to manage, and it's what I've come up against in C3.
In the example you give they both have the same MyGame name in the filename anyway, followed by a version number. I don't think many people will call their game "Jungle Adventure v1.c3p" and then make version 2 and not call it "Jungle Adventure v2.c3p".
If possible, please consider including the display of the filename somewhere if nothing else. It makes it very hard to manage large numbers of files. It's always best for users to have direct control over and awareness of their files. If the filename were visible then the issue of whether to derive the project name from the filename would be a moot point really. Users who prefer to focus on the file name would just do that and ignore the project name. The project name has no relevance when managing the actual files on disk though, which is what makes file management so difficult. You have to syncronize everything, and track changes, and then you can't even see the filename when you're working in the editor.
Please don't get me wrong, I absolutely love Construct. It's genius, and hats off to you personally, just IMO this is a thorn in an otherwise brilliant product, and I haven't encountered many other thorns, which is saying a lot for such a robust product.