Currently in 20.10.x Incremental tables with deletion handling get an Is Tombstone field that is a bit type, History tables with deletion handling get an Is Tombstone field that is a bigint.
In 6xxx I cannot seem to get any kind of Is Tombstone field, so the inconsistency is more that there is no way to know that a record was deleted in source
If you add history to an existing incremental table with soft deletes, you will be forced to use the history soft deletes which will change the type to bigint. I think it would be good to make this uniform and add some kind of check to the upgrade advisor tool. You'd really want users to get a reminder that they need to check dependent project objects.
Apart from this issue there is also the fact that a bigint is fairly expensive for a field that has a boolean meaning. Given that less that 9 bit types mean the values are stored in the same byte, this would be a performance benefit, especially for large Fact tables. If users want to count deletions they can cast to an appropriate int subtype in their transformations.
So in summary: choose the same type for both incremental and history soft deletes. Evaluate which type would be best, my suggestion would be bit.