Nice style Alex! I do appreciate what Mind Cafe is going for. They do it for the same reason I do it, for branding.
I've been self-publishing a lot lately, so I haven't had much issue with that.
You could certainly check with the publication owners/editors if there could be a common ground. I love what Amardeep is doing with using the colors of the publication he publishes in. Some publications would be open to that for sure.
Otherwise, as proven in one of my previous articles, the writers make a publication, not the other way around. All the top publications are top publications because of the people who right for them.
So, if they won't take you because of that, tell yourself that you're doing them a favour by writing for them, not the other way around.