That old 18" raised requirement still applies any time you're putting a gas appliance in a building with cars or other stored gasoline. You really don't have to make a super heavy pedestal if you can core drill the floor and put in some cement filled pipes at all four corners. Anytime, in a commercial environment, where an appliance of any type can be bumped by cars, forklifts and stock pickers it's generally always a requirement that it be protected in some manner. Sometimes this means constructing a wall, fence, or adding pipes in the floor.
There's nothing really in the fuel gas code (for commercial) that is much different at all than what's in chapter 24 of the IRC (for residential). These codes go on and on about pipe sizing and venting requirements, with very little about the actual fuel gas piping. It seems that you're particularly worried about protecting the CSST (flex) where it emerges from the ground. The only requirement is that the conduit sleeve extend at least 2" above floor level. These codes make almost no distinction between black iron pipe, copper, and CSST with respect to their ability to protect against physical damage. Common sense should prevail, however, and would cause one to arrange the pipe work in such a way that it's likelihood of being damaged is reduced. The flex can run the whole way to the gas valve (with a shutoff installed). In fact, it's generally a good idea that the final connection to any equipment that vibrates be flexible. There is also a requirement that the space between the flex and the conduit be sealed. There is commercially available compound to accomplish this, but the trade name of it escapes me at the moment.
I can't really pin down a good online reading resource for you. You see, there's the "2003 International Fuel Gas Code" (from which the IRC takes it's gas section) and the "2002 National Fuel Gas Code". Neither one is very different than the other. Both must be purchased, so there's little text from either online. When it comes to commercial work, there's little self help information out there, since engineers want to keep all that information close to the vest. We try to help here as best as we can.
"Nothing is foolproof to a sufficiently talented fool"