You can temporally use "si off" to turn off the structural integrity check while you shore up the supports.

I've toyed with a few mods to it, but nothing that passed 'the test' of both an SP and MP playthrough. Most of the placement problem is in Empyrion's quirky footprint system.
On the upside, it looks damned nice jutting out from a mountain if you can shore up the supports before it collapses (which I've had happen a few times heheh).

I know, it's kinda annoying.
I added an extra layer of blocks to the bottom just so it could be sank and I would not have to dig it out.
… and I end up having to dig out sections after I spawn it anyway.
I have been debating on adding an additional layer to the bottom because of all the times I and up digging it out.

I've used this one, buried into hills and mountains, to the point it's been nicknamed the batcave. :)