Firstly, the important thing to realize is that a 288-line resolution will always be taller than a 240-line. This is unavoidable as the spacing between the lines on the monitor will never change, unless you adjust the height control. The only way to get an absolutely true resolution for running vertical games on a horizontal monitor is rotate the monitor. So running vert on horiz, we are starting out with a compromise. So, what I do is adjust the monitor so the horizontal games have small top/bottom borders and the verticals are slightly cut off, not enough to affect the game.
Another way is to adjust the monitor for perfect horizontals and enable hardware stretch for the verticals. Then the verticals will fit exactly but will be degraded to the quality of a regular VGA card.
The auto-pan is only useful on the Windows desktop. All it means is that you can run at a low non-interlaced (hence no flicker) resolution, and then pan around the screen, rather than having the whole desktop visible but flickery. Note that arcade monitors cannot display more than 300 lines so 640 X 480 must be interlaced.
It is just about possible to display 800 X 600 interlaced but it's pushing the monitor timings and some picture distortion might occur because the beam might not have enough time to fly back to the top after each frame.