Hello!
Functionally, they are the same (lack of) phylum. The difference is that, for d__Bacteria;__ the classifier couldn't assign any taxonomy beyond the domain level; whereas for d__Bacteria;p__ the classifier found a match but that match is not annotated at phylum level. So, long story short: yes, they can be understood as the same on a practical level. This post addresses the same issue.
Yes you could merge them into one "Unclassified" phylum, although I personally prefer to get rid off these too general taxonomic annotations. I came to this conclusion when I asked this question a couple of months ago.
Sadly there are a lot of bioinformatic work out there with a Methods section that does not allow replication due to too shallow explanations (not to mention those with no shared code at all...). I suppose this is because a lot of people still think of bioinformatic tools as a black box, and they follow default steps with default variables that they assume they don't need to mention in Methods. Anyway, if you want an example of a Methods section where this filtering is stated, here you have one. From its Methods section:
The table and sequences were filtered to exclude any ASV without phylum-level annotation or which could not be inserted into the phylogenetic tree.
I hope this is useful for you.
Best wishes!
Sergio