Yes, actually there are reasons for each of those. The cape is part of his kryptonian culture. Jokers purple attire perfectly encapsulates the characters mindset and outlandish nature. The reason to have a bat on his chest is for to engrain the mythical nature of the symbol into the hearts of criminals as a symbol they should fear and as a symbol of hope to citizens.
The importance of trunks? It gives us more evidence for Bruces lunacy? It's a handy adult diaper so he can go all night with no bathroom breaks?
So yes, intelligent movies use things for a purpose, what you're asking for is blind fanboydom, which is fine, but hardly a reasonable argument for including the trunks. I'm not saying there's no way to include them, I just haven't heard anybody give me a good one despite the purported 'need' to include them and personally most of my favorite depictions don't have trunks.
And your comment about the perception of the ga not mattering is adorably naive. But also the majority of batman fans on this board seem to be against trunks, so then it's catering to a very small minority for pretty much no gain as they'll be seeing the movie either way.