Of course yes & why not ? So much so even the marriage amongst the sub-sect classification within Iyers ( such as Vadama , Bracharanam, Athista ) are acceptable. All these sub-classes are time related creation .
Just as a reverse logic , having accepted the Gothra theory - it is foolish to distinguish a Bhardwaj Iyengar is any different for Bharadwaj Iyers. In the past the customs and traditions ( for Homa Samskaram ) deviated from one sect and other. It is only the acceptability that matters and anything is dogmatic and superstitious.