This is currently solved for me as I reverted to Brave’s current version on Google Play Store (1.39.123, Chromium 102.0.5005.125) and in that version the flag needed to disable the new window option is still available.
Although it might be solved as of now, I would greatly appreciate if there was some sort of workaround as the flag will certainly disappear in future versions meaning as soon as Brave upgrades to Chromium 103.
This certain flag Show a menu item 'New Window’ is only available if you enable Temporarily unexpire M100 flags.
I hope that as long as I don’t uninstall current Brave version and only update through Google Play Store, the flag will remain disabled but not visible in brave://flags.