MDEV-23855 InnoDB can do checkpoints much more rarely. This improves performance under write-heavy load, but makes mariadb-backup create huge incremental backups (since the last checkpoint).
One way to solve it would be to let mariadb-backup to force an InnoDB checkpoint before a backup. There are many ways of doing it, innodb.page_cleaner test shows one of them, Marko Mäkelä knows more. Perhaps it should be optional, but, likely, enabled by default.
Alternatively, InnoDB can force a checkpoint automatically when entering a certain backup stage.