I don't care about the boot loader. That is just a single call to grub-install (or so), to recover that. And the partitioning might be different on my new PC anyway, or in any case I would want to decide that customly when recovering. So these are no reasons for me.
Are there other reasons not to use Perkeep for a full system backup? E.g. speed? Overhead in size?
I'm interested in the history only for some subset of the files, though. Is it possible to remove the history later on for certain directories (e.g. all in /usr)?