The word "disagree" is intransitive so why in this sentence
It is unusual for you and Tom to disagree"
is there no "with" or "upon" to follow it?
Is its meaning the same as "It is unusual for you and Tom to disagree with each other"?
Intransitive verbs do not automatically require any with, upon or other type of complement. If the additional information is needed, it can be expressed. If it is not needed, it can be omitted.
It is unusual for you and Tom to disagree.
One of two things are happening here:
The speaker/writer is assuming the listener/reader already knows what you and Tom are disagreeing about.
This sentence can also mean the same as "It is unusual for you and Tom to disagree on anything" or "It is unusual for you and Tom to disagree in general."
At the risk of being wrong, I have to say I do not understand your own question.
Because disagree is an intransitive verb, it does not need an object, and therefore, does not need "with" or "upon" to follow it.
So, I'm not sure why you want to force it to have one.
The reason "with" or "upon" follow "disagree" at times is because of the object, not the verb.
Does this help?
If the subject of the verb disagree is both people, than it means they have different opinions:
Bob and I disagree on this matter.
If the subject is only one party, than you use with to link another party who the subject disagrees with:
I disagree with Bob on this matter.
In your question, the actor is both "you" and Tom, so the sentence is correct. It can be reworded, though:
It is unusual for you to disagree with Tom.
As for upon, it is intended to explain further and introduce the matter people disagree on. If you are not talking about a particular matter and want to say that people just often argue (or if the matter is clear from the context), then no upon/on is needed.
Keep in mind that such constructions are possible:
Bob and I disagree with Tom.