I was just wondering if they will be incompatable together?

We will see. We have practically no information as to where the house is located in the game world, or what it uses to do so.

It's not gamesas's job to make sure that their DLCs do not break mods. So, popular or not, they're not going to check or work around it.

Well, Build Your Own Home is limited to a single spot, and Hearthfire doesn't seem to be, so it seems unlikely.