Wow, did you get this idea now, just by thinking about consequences of centering around one intention? Because it's not obvious and to some extent definitely true. Yes, there is a stage of integration where 'difficult stuff' comes up in the mind. In Culadasa's stages of concentration development it corresponds to stage 4 mostly (laid out in details in his Mind Illuminated book).
However:
- When you're doing it right, it's happening almost automatically, there's often pleasure of concentration that eases things significantly, and the relief that comes up... it's worth it. With time you almost yearn for such difficult things to come up from the depths, knowing the relief and completely new perspective that the integration will bring about.
- Saying that "I don't want to integrate the difficult parts" is a bit like "I don't want to be completely happy". Unifying the mind is like unifying the world - no conflict, completeness, content, everything you want and love is right there with you.
- Integrating the difficult parts is not just getting over them. Sometimes it results with ability to transform difficult relationships, to forgive, to reach deeper levels of communication with eg. difficult parents etc. What's mind changing is world changing.
With all that said there's so many examples of meditation gone wrong, of doing things that are counterproductive etc. - there definitely are less and more smart ways to do it. And hopefully the marriage of Buddhism and the Western thought will result in further advances.
I'm almost sure that neurofeedback will be of some help - we learn so much quicker if we have tight feedback loops, with immediate feedback it's almost like a game. Even in the paper you cite, the best results were achieved during the 'free play' phase, were one could play around interactively with the graph.
In the meantime I recommend Culadasa's method because it's very precise, driven by joy and the articulate, clear style expands to the whole community, which can be helpful when someone gets stuck.