When creating a note on a transaction, is it possible to have a field on the note to reference from what transaction it was created?

What do you mean by note?

The ones found here on records

Wouldn't you be on the transaction that the user note was entered from?

Yes, but if we want to see all notes from the customer record it does not specify which transaction the notes relate to which is annoying

I understand, I didn't know you could look at "all user notes" from the customer record.