I can't speak for the FSF nor for the GNU project. I think you can do these courses, although this will probably make people believe that you support or are willing to use the non-free systems referenced in the certification, if you do mention to the public that you do have that certificate.
In my curriculum and/or resume, I remove all mentions to non-free software in my fields of interest (mostly: organization management, accounting, graphics design, and basic education on computer usage (no certification for this one because I'm not a teacher)). I had taken a course about basic Windows usage (they labeled it as "Basic computer usage"), and about all that non-free software used for graphics design, but all this was when I wasn't a free software activist (I was just studying the movement). Nowadays, I simply refuse to take courses about any non-free software or non-free system distribution. I do feel the need to take at least a basic course (with valid certification) about most software I use or plan to use (like: GnuCash, LibreOffice, Inkscape, GIMP and so on). However, since I'm currently unemployed, and I don't have a monthly income that is reserved to my own use (I do receive monthly incomes but they go to other stuff, like college expenses), I can't afford to pay for the courses even if I would find one (because I haven't found courses about these software, and when I do find, it requires non-free JavaScript or non-free software in order for me to access the course and materials). So most items in my curriculum and/or resume are all about self-taught free software usage, and most of the items let my skill levels transpose to the reader/evaluator. For example: If I'm self-taught on *basic* GnuCash usage, why would I lie to the reader by briefly saying that I'm just "self-taught on GnuCash usage"? And by this, I hope to, one day, be chosen for what I really like to work with. I really wish there would be a place where individuals could place their free software-related curriculum and/or resume. Actually, I think GNU Savannah *does* have this feature (I'll look for it later).
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