Those are great questions!
As of now, there is no other ways to manage a large number of modifiers, the modifiers list was not yet modified to account for managing them, unfortunately.
MCG is part maxscript and part c#, the c# part (librairies) is not portable to maxscript, so that is not doable. It is possible to extend MCG with Maxscript, in two ways; there is a node called 'EvalMaxscript' in MCG that enables maxscript calls to input values into the graph, and there is a CustomUI tab in the graph properties, initially intended to enable UI editing and adding but also support extended maxscript functions.
MCG graphs can also be called from maxscript, to create, assign or set parameters to MCG graphs instances in a scene. MCG also has a Maxscript function output, MCG can be used to create maxscript functions.
There is an "output: geometry". This output do enable some type of management, from the graph properties, the "Category:" field lets the user defined a "group category" that is added to the Create Geometry panel drop down list; i.e. added inside the [Standard primitives, etc.. , <user MCG category>] drop down list, and that category will hold all geometry graph tools that have that category set in their properties. The geometry output 'can' be used as a modifier to some extend, by using a pick node parameter to have a 'base object'; but that limits to a 'single' graph and not a suite of modifiers on top of each others.
There is no 'live' mode as per say; for now MCG graphs do need to be saved to file prior of existing in a scene. But once an instance of a graph is created in the scene, it is updated each time the graph is saved and evaluated; so one could start with a 'simple' graph, create an instance of it in the scene and build from there; you'd see your graph changes right away once saved & re-evaluated.
If you did get a chance to see some current users graphs tools, it is quite amazing to see what users get to do with MCG! 🙂
I hope I was able to answer your questions ! 🙂