The software you use will allow you to select the format; however, not
all software offers both. The most popular software now for HDR video is
DaVinci
Resolve Studio
(must be the Studio version), and it offers both formats, as well as a
third—Hybrid Log-Gamma (HLG), which is not as common. Among other
applications supporting HDR are SGO Mistika, Adobe
Premiere Pro, and Avid
Media Composer.
Furthermore, within each format, you can also select the output codec.
Premiere, for example, lets you choose between DNxHR, HEVC (H.265), and
OpenEXR.
Does any flavor of ProRes support the HDR
requirements? I would certainly transcode. I just thought ProRes was
limited to non-HDR (0-1024 luminance range) workflows.