NCSY and kiruv, in general, differ from the norms of frum life in certain aesthetic ways.
As you noted, guitar havdalah is an example. Nothing I can think of that really prohibits that, but it’s not done, because I think we generally are reluctant to have musical instruments in a shul (even though Carlebach did it, and of course, we had in the Beis haMikdash).
Other things, like goyishe music and dances, are done to be hospitable to the non frum. This makes it unacceptable to people FFB.
I think gradually as they grow they get acclimated to the normal way of doing things. Like when a person graduates from the beginner’s minyan to the regular minyan, for instance.