I've been doing installs on vehicles since 1998, both on my personal vehicles and professionally. I've had 2 vehicles leased that a minimum of 2 holes either on the trunk or on the roof (one car, one truck) and I never got pinged for the holes. I always removed the mounts and put in hole plugs to replace them. I never got pinged on either one when it came time to end the lease.
Also, on a number of the government vehicles I've worked on, local, state, and federal, were leased vehicles and we always drilled 3/4" holes for NMO mounts unless we had an unusual situation where we had to use a 3/8" thick roof mount. Matter of fact 2 different counties that a shop I worked at had contracts with had mandates in the communication SOG's that said we had to do a permanent roof mount on all vehicles unless it was an unmarked/undercover unit. Of course the federal vehicles we did (FBI, DEA, etc) you'd never have known it was an LEO vehicle anyway.
Just my experience, DRILL ON !!! Especially if, just as someone stated previously, you want any kind of decent performance. If it's just a scanner then you can most likely get away with a trunk lip mount or something on an L-Bracket.