You've got it backwards. They're dissolving their old non-501(c)(3) Foundation that they use to manage their finances currently, and becoming a part of an existing 501(c)(3) called Software in the Public Interest (SPI)
TL;DR from the article, they're doing this to:
Offload the overhead expense of independently managing their finances/accounting, by merging with someone who already has a robust system in place
Save money by becoming tax exempt
Allow themselves to accept matching gifts from donors whose employers support such things
I think, regardless of where you're donating from, this means less overhead and your money goes a little bit farther on the charity's side, which is a win for everyone.
You're right though that it's not tax deductible for you, so the amount you can donate does not change, just the effectiveness of those dollars.
Reading between the lines on the gentoo-dev mailing list, I gather that the old system just was not working very well, with friction between the Foundation and the technical side of the distro.