cherrybim, the rule is the couple follows the minhugim of the Choson. If this will cause machlokes, its best to be moichel (like you said.)
Many of the minhugim you compared to the goyim, are things the goyim copied the yidden (not vice versa.)
“Rosh Yeshiva families with mixed seating and no mechitzas”? Which Rosh Yeshivos?