This is my solution. others may have additional...For this run-through, let's assume I want the plotted text height to be 0.1 units.
1. Create a new text style. Give it a name (I'll use Test-0.1). Check the "annotative" box. under Height, enter 0.1. Pick "Set Current" and close the dialog.
2. Go to the layout tab where you have your two viewports.
3. Double click in one of them to access modelspace from the viewport. Place some text using this newly created text style. It should be 0.1 units relative to your paper space.
4. Now look at the lower right corner, just right of the viewport scale. One of the little trianlgle like things has a lightbulb on it (this is ANNOALLVISIBLE). Turn it off for now (non yellow lightbulb that is).
5. Pick the text object you just placed, right click, hover over annotative scale ('annotative something' - sorry, not at cad computer right now), and pick Add/Delete scales.
6. in the dialog, you will see a list of scales that this text object has. Pick Add, and add the scale of the other viewport to it. You should now see two scales in the box.
Close the dialogs and you should see the same text object at the same paper space height in the two viewports, each with different scales. Note that if you pick this object, you may see both scales while it is selected.
There are other variables and things to mess around with to maximize your benefits with annotative scales, but see if the above steps work out first. (I would also leave the button to the right of the 'lightbulb' turned off - this is ANNOAUTOSCALE, and if on, you will end up with a mess of scales in the drawing).
Hope this helps and works out. If not, repost and the pros around here will set you straight.