the definition of "can this be done inside the tool" is a bit of a hit and miss concept really.
I mean, dimenstion shift still loads in nesmaker and i do still use it for script editing and drawing screens, but vast majority of the code and functions in the game are no longer managed using nesmaker's UI.
I simply use Nesmaker as I would use any other tool for assisting in development, some people draw screens on shiru's screen tool (as do I for special screens like menus) but I just use nesmaker for stage design instead of suffering with manually writing nametables. Same goes for editing scripts, I could just use notepad for it, or whatever text editor, but since its all nicely organized in nesmaker, I just do my script editing with that instead.
as for parallax, as CutterCross said, I use it extensively and just like any other custom piece of code for any nesmaker project, a parallax can be added. Our DMC IRQ splitter is just a software scanline counter controlled in code.
the documentation for using DMC IRQ's for midframe splits is all available in nesdev wiki, https://wiki.nesdev.com/w/index.php/APU_DMC and our code is directly based on this theorem, nothing prevents anyone else from implementing it into their games.
https://www.youtube.com/watch?v=J0yg9mg-QNk