Many iterations ago, GB did not support metaboxes. That was what I reported at the time. Since then, metaboxes seem to have been fixed in the GB plugin. But you assume that they will work when GB is merged into core (which is shortly to happen).
That assumption appears, however, to be false. You can see the mess they are currently in here: https://github.com/WordPress/gutenberg/pull/8762 and here: https://make.wordpress.org/core/2018/11/07/meta-box-compatibility-flags/
Even if they manage to get that fixed at some point, my guess is it will break again because the underlying architecture of GB is insufficiently robust to enable one set of changes to be made without breaking other stuff. (That's why moving it from a plugin to core is so problematic.)
What you decide to do about all this is, of course, up to you. My own decision has been to join the team at ClassicPress and avoid having to play roulette.