The pen tool doesn't care how much contrast there is. The pen tool should work accurately on a solid grey layer. I have never seen the pen tool refuse to put a point where you want one. Perhaps you're calling something the"pen tool" that is different from what I call the "pen tool". Could you show some screen shots to help disambiguate things?
If you have the rotobezier tool selected the points are tension points. If you have rotobezier deselected the pen points are corner vertices. I think you may have rotobezier selected.
I am definitely using the Pen tool and the add Vertex tool to add additional points that I later drag into place. I think part of my problem was that I was just not zoomed in enough, after zooming in, it seemed to help with it not wanting to plot the points.
1. I also have the RotoBezier checkbox selected. I thought this option was better with making curves around a shape?
2. I'm not entirely happy with how believable my masked shape appears. I tried adding motion blur to it, I also played with the Mask Feather to soften the edges. Is there anything else I can try?
3. Is there a way to temporarily hide the individual effects like Mask Feather, Mask Opacity, or Expansion to see before and after comparisons?
For some types of roto work I prefer to have robobezier selected but the points are only on the line if you hold down the ALT/Option key to reveal the V shaped tool and increase the tension to pull the tension into a sharp corner so your behavior is expected. Here's the important part, the points of rotobezier are NEVER on the line of the mask unless you increase the tension of the corner to the maximum so your observation that the points are not accurately positioned is accurate. Only Bezier points paths have the points attached to the mask line all the time.
The trick to using rotorbezier is to use as few points as possible and gaining experience in using the tool. Take a look at this short video that shows how I use a colored solid with the blend mode set to multiply as the source for my roto work. I picked the orange color because it let me see through footage clearly. I also stabilized the footage using AE's stabilizer to remove motion of the dog and keep the dog's eyes pretty much in one place. This makes it easier to do the roto. The stabilization will be removed once the roto is done. and the motion added to the solid layer. This will give you an idea of how to set the initial points, start setting keyframes and refine the movement. If you carefully watch how I'm using the mouse and the alt/option key to grab mask points and adjust the tension of the corner points you'll learn how to do this kind of work. BTW, there's a lot better way to put the motion back into the clip than the one I showed in this video. I just didn't include sit, but will in a future video.