I’m not an advanced modeler, but here’s my personal experience. I think it’s not always a bad thing to let your meshes intersect if it’s not an important area. However, when it’s possible to keep good topology, I try to make my things connected, so when I add a subdivision surface modifier, the transition becomes very smooth and you can edit it with edge loops if you want to have just a little bevel. An alternative is having just a little distance between two meshes and adding a back face for nice occlusion shadows, just like Kent explained in his “Wall of Mailboxes” course. If you really want a very nice and clean mesh, I would use on of the two options I mentioned.
I hope this answers your question!
