"flatkey" refers to the type of krypto or OnGuard locks that replaced those with tubular keys. The tubular keyed locks could be picked with a Bic pen, that's why there was a "scandal". The flat keyed ones are extremely difficult to pick, but they can be physically compromised, just like the old tubular keyed ones. However, physically compromising a high-end lock is a VERY time consuming/difficult process that may require special tools.

Two locks (one for rear wheel/frame, one for front wheel) is about as safe as you can get as far as locking a bike. Maybe taking the front wheel off and locking that in the same lock as the rear wheel would work too. Everything else comes down to methods: locking up in a visible area, with reputable people around who will notice if somebody is messing with it, etc.

Also, some people use a length of bike chain wrapped with inner-tube to secure the seat to the seat-stays.