You're welcome.

If you're practicing the A minor scale, then A is 1 (C is 3 in this case).  Whatever scale you are practicing the root note is always 1.  It's important to think in terms of interval distance from the root note because that's what gives a scale its distinctive sound.

I think you might be conflating scale intervals & the musical alphabet, but they are two separate entities.  They are both absolute & do not alter each other.  The notes (A-G#) are where they are regardless of any scale.  We simply use them as a static pattern to call out the notes when we land on them when applying any scale pattern.

The distance from the 1 (root note) of any minor scale to the minor 3rd of the scale is always 3 frets (or one and a half steps).  Then wherever it happens to land on the musical alphabet, that's what note name it is.  A to C is 3 frets, so an interval distance of a minor 3rd. It's just a matter of systemic coincidence that the A minor scale is the only one with no sharps or flats.

Let's say we're playing the G minor scale.  

G (1) ws A (2) hs Bb (3) ws C (4) ws D (5) hs Eb (6) ws F (7) ws (G (1)

In this case we start on G and if we go up 3 frets to the minor 3rd we land on Bb.  So in this case we find that the minor 3rd of the scale does happen to land on a flat note.  But we don't make the B a flatted note because of the scale.  The notes B and Bb are where they are regardless of any scale.  And that's just where we land if apply the scale intervals.

I cover moveable scale patterns in these tutorials.

Major Scale Patterns https://www.guitartricks.com/tutorial/453/

Minor Scale Patterns https://www.guitartricks.com/tutorial/887/

Hope that helps!