A little extreme, but in one installation I did in the past, the alarm brain was installed into a custom welded steel case, with a shatterproof lexan cover underneath the spare tire in the trunk. Wiring from the brain was routed through a flexible metal sleeve popular in home electrical wiring. I found it difficult to cut thru without an axe, most car thieves conventional tools would not be able to penetrate the case, lexan, or protective loom within a reasonable time for theft.
When the wires reached the front of the car they were all well concealed. Every effort was made to locate the necessary wires away from the driver's side dash and the fusebox. Well you are limited on the starter kill wires to the ignition, but it was backed up by a Clifford wireless immobilizer on the fuel pump. Also the wires werent routed as one would expect.
Even to a BMW technician the alarm was undetectable in the car because no taps were apparent. Everything was done behind the dash or metal protective panels, or very discretly in the engine bay.