This spell is the only official mention of "Unholy Water"
A quick search on D&D beyond, the official D&D 5e web toolset, reveals that the Commune spell is the only official mention of the term "unholy water".
That means we have to fall back on natural language
Since the term has no official game meaning (because it is only mentioned once as a spell component and nowhere else), we have to use the natural language definition of the terms.
Unholy water is, obviously, water; it's in the name.
Dictionary.com defines unholy as:
1.
not holy; not sacred or hallowed.
2.
impious; sinful; wicked.
By this definition, unholy water could just be water the isn't holy water. However, this would mean that something like tap water could be used as the material component of the spell. Since, Commune specifically allows you to talk to a deity or divine proxy, I would argue that this non-religious/non-divine definition isn't what is intended.
So, based on the second definition, unholy water is some way the opposite of holy water. Where holy water is water that is blessed and carries a positive religious connotation, unholy water is profane, wicked water with a negative religious connotation.
RAW however, that means unholy water doesn't do anything
As you have noted, there are no rules for creating "unholy water". There are no descriptions of any mechanical effect that it has, or any uses for it besides this one spell. RAW, it is simply used for the Commune spell and nothing else.
It has no other properties RAW, and any other mechanical effect given to unholy water would be a DM call.
No, there are two different, but similar, ways to create holy water
One method, outlined in the PHB under the description for holy water, is not a spell but a special ritual. The other method, outlined in Xanathar's, is a cleric/paladin spell.
One subtle benefit to having a spell and non-spell way to create holy water is that non-cleric/paladins can gain access to the ability by taking the Ritual Caster feat for example.1 Also, the non-spell version will allow a cleric/paladin to be able to create holy water even if they do not have the spell prepared or are out of spell slots.
Yes, they are very similar, but that does not mean we can assume they are the same thing. Nowhere does either ability reference the other or link them in any way save similar wording. In lieu of official errata or clarification saying that they are the same method the only way to treat this RAW is as two different ways to create holy water.
Jeremy Crawford also supports this reading:
The description of holy water tells you how to make it. If another method for creating it appears, that's merely another option.
1 - thanks @HellSaint
Best Answer
Your spell component pouch counts here if the DM agrees
The description for a spell component pouch says, "...has compartments to hold all the material components and other special items you need to cast your spells, except for those components that have a specified cost..." (PHB. 151). The description does not say anything about the pouch being magically filled or having an endless stock so it's really just a conveniently designed pouch for holding things your character gathers in the background.
You regularly cast Bless which has the material component, "a sprinkling of holy water", (PHB 219) so that's available in your pouch. The pouch description doesn't say you've got an infinite amount of it so this isn't some loophole to get free Holy Water flasks, it's just a point of convenience.
Flameskulls, "...reform unless they are splashed with holy water...", (MM. 134). Now strictly speaking you need a splash of holy water and your pouch contains some undefined number of sprinklings. Fair rulings would include that you don't have enough holy water (bit boring), that you've got just enough and now have none left to cast bless (add tension), or that a sprinkle is good as a splash and inspiration for your troubles (reward thinking about your resources).
You'll need to talk to your DM to figure out how this will work at your table.