Not really... see the shipsets we make are still part of the "part sets" of the default races... which then also have their default race ships.
SO for example, I've made 20+ shipsets, and not only do I have sets that "cohabitate" menu space with the default designs for a part style... like Drengin... but multiple other sets of ships from other shipsets of my design because I've been forced to "double up".
There are filters though, to filter out "core designs" and this works and should then make it more enjoyable for you.
I hope that made sense.
PS: I've never successfully tried to make a new parts style, to then apply a custom shipset to... but if it's possible, that would solve your issue.