So the 1971-72 dodge chargers came with stainless trim for vinyl top option. For the full top, there is a trim piece below the rear side window that leads back to the ‘V’ trim. On the 1972 Charger’s with SE trim option, would that same piece be the same length or different due to the smaller side glass?

The side glass on the SE and non-SE are the same glass. They just cover the glass on the SE with a sheetmetal panel and shorten up the drip rail. The vinyl trim would be the same as on the non-SE as the SE, BUT....... there are two different trim styles depending on if there is window sill stainless trim or no trim on the sills.