DAR is perfectly fine to use, as long as the entire image (including any borders) is included in the calculations. Thus, all images from the same system should end up with the same scaling factor.
The pixel aspect ratio is not affected by how large the active display region is. Displays can't even detect the border if the border is at blanking level black as older systems tend to do. It's determined by the horizontal/vertical timings and the pixel clock. Those can be compared to the specifications for NTSC/PAL square pixels to calculate the resulting display size and aspect ratio on a standard-tuned display for a given image pixel size.
About the only way to properly calibrate what the borders "should" be is to calibrate the TV to what would be a reasonable approximation for SD TV signals, and POSSIBLY make small adjustments after that point if the computer looks wrong.
Even then, every TV is going to be somewhat different and so there's a huge amount of variance on how it's going to look in the end. Same applies for computer monitors back then, though calibration of an RGB monitor is going to be even harder than composite since you can't easily run a VCR over it to try to get SD TV calibration.