You're absolutely right! The basic software infrastructure that can be adapted to safely and securely handle user data is completely free.
It may be worth considering that adapting said FLOSS software, doing the requisite custom integration work, and then doing a large migration successfully might all be perhaps slightly less free than the software you correctly and wisely point to.
There is no monetization concern here, the project is sponsored by Framasoft, a French non-profit organization who wants to provide free-software alternatives to services owned by big corporations.
I would argue that if some software is under a free (libre) license, it's worth using over [non-free] first party stuff. This doesn't apply to f.lux, but does to redshift.
That's good but does it actually avoid patent minefields that others scattered around? That's equally critical for healthy adoption.
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