A custom tileset is fine. I'm not sure how you would go about integrating it. BronzeAge uses monogame, and the tilesets are processed through the monogame import pipeline. The imported files can be found at "Bronze Age\Content\tiles". I suppose if you imported your own files you could just replace them there.
What sort of tiles did you want to replace? Some of the tilesheets have a more complicated format than others.