I have the same issue, it should be solved by the bootupd migration. Changes/FedoraSilverblueBootupd - Fedora Project Wiki
Relevant issue: Use bootupd and remove ostree-grub2 (was: All deployments are shown twice in grub) · Issue #120 · fedora-silverblue/issue-tracker · GitHub
Running sudo grub2-switch-to-blscfg migrated the grub config and removed the duplicate entries for me on Silverblue 37 (installed as 36). I’d imagine new installs from 38 up won’t have this issue anymore.