Well, what I have set up is partially what you're describing, and another part of what you postulate is actually made moot with such a plugin.
For my N64 TASing, I use this USB dual analog controller:
I have the left analog stick to control the N64 analog stick, and the right stick to control most of the yellow c buttons.
I have the input plugin set up to receive direct input from my controller. I can either use the mouse to drag the blue dot and have the plugin hold the tilt/angle there, or make the controller control the game. Each of the buttons are configurable, and I have them mapped out for the A, B, start, R, L, Z. one button is pause/unpause, another is frame advance (which I use another program to enable, will go into detail later.)
So I have the input plugin, which when in frame advance I can use it for high precision maneuvers, have it hold down buttons for me (like A for driving in Mario Kart 64.) I have the controller, which is binded to the input so the game accepts input no matter if I do it on the plugin or the controller, and I also have my keyboard, which I use for pausing and frame advancing (I have my controller set up so whenever I press the FA/pause button, it makes the computer press F or D on the keyboard. I switch between the controller and the plugin at a consistent rate, and use F or D on my keyboard if I need to hold down frame advance or make many frame advances very fast.
Now, how does it help with 2 player TASing? By completely freeing your hands. Having the two windows helps in not playing "Twister with your fingers" to get all the key presses right.
So, um, I guess in closing, having the buttons pressed for you on the screen on a control panel window will save time and energy, and prevent finger achiness for multi-controller runs.
As to why some oif your suggestions aren't needed, the controller can be binded to register on the plugin if you press the button on the controller, and the whole point is to free up the fingers to use only the mouse for checking the boxes to be registered as held down... your suggestions are, initerestingly what the plugin can already do.
if you left click on the box, it becomes held down.
if you right click on the box, it turbos.
Having this window on top of the screen all the time can be a little annoying sometimes, but when N64 TASing it is absolutely invaluable, giving full 360 degree movement and other wonderful features.
However, when I was working on a N64 run with 2 controllers, 2 control panels would appear for each controller. Having done a few wips of some other 2 player runs on other systems, I found using this plugin to TAS with two characters was FAR easier than binding 2+ characters buttons to the keyboard. For some games, I was able to reduce the size of the control panels and easily fit 4 such windows on my screen at once, with the emulator still visible.
I found making a 2 player run with this plugin to be far easier than I had ever thought. I was making faster and better progress than other 2p runs I've tried out. It has automatic auto-hold capabilities, and allows for a greater flexibility in testing one character's movement, and then to simultaneously do them at the same time. The plugin was more about using the mouse to press down and hold what buttons you want, instead of straining your finger's flexibility in how many buttons across the keyboard you can press. Having a separate window for each of my characters made the run so much easier for me to make, I believe that such a feature for other systems would benefit 2+ controller runs.
Does this sound like a good tool to assist runners with 2+player runs, and would such a feature for a separate control panel, maybe mocking the system's controller, to appear as an option for those that wish they had more freedom with their fingers?
