> The fact that the upper reaches of a dome are almost all wasted space...

Not psychologically, it's not. You might say the same about much of the inside volume of a cathedral; useless space! And yet, we make sure they all have it, because we value it.

> because the pressure difference between inside and outside will explode your habitat before any self-healing mechanism kicks

No, it won't. It's (at most) one atmosphere worth of pressure. ~14 psi. A small hole in a tire doesn't immediately burst it, and it's under significantly more pressure.