Most people using the Librem 13 use it as a portable workstation and value battery life. And since no one really want a slow SATA drive now anyways, would be useful if you get rid if it altogether. It opens up space for at least another 15Wh worth of battery which could extend battery life with a minimum of 1.5 hours. And that is significant.
My SATA port right now is empty. I only use a fast and power efficient NVMe SSD. I suspect Librem 13 users will happily live with this compromise. Especially since SATA SSDs are marginally cheaper if not more expensive than NVMe drives and a combination of a smaller NVMe + SATA does not yield much savings.