The issue is that prolog primarily uses unification to do computation. To get it to do arithmetic operations you need to tell it to do so explicitly using the is operator.
So, in your first program you explicitly tell it to perform subtraction with the clause N1 is N - 1, so that works as expected.
But in your second program you are not asking for arithmetic computation, but unification, when you wrote fact(N - 1, R1).
If I had the fact fact(5 - 1, foo). defined, then I could query for ?- fact(N - 1, Y), write([N, Y]). and prolog would happily unify N with 5 and Y with foo. This query would output [5, foo].
So, to go one step further, if I had the fact fact(foo - bar). then the query ?- fact(X - Y), write([X, Y]). would happily unify and return [foo, bar]. The - doesn't denote subtraction - it's part of the structure of the fact being represented.
fact\2to evaluate its first argument each time, and get around the problem in the second version, but it is more conventional to do as you have in the first version (evaluate before passing). The flexibility of Prolog to manage "lazy evaluation" of arguments is potentially useful, but the factorial computation is too straightforward to take advantage of it.fact/3) to make this work.