Flexible gas connector on furnace

I am working on my furnace. I bought a flexible gas connector that will run from the end of my old black iron pipe to the new control valve. The only way it will fit is if I go through the furnace housing. I plan on using grommets to protect the line from rubbing against the housing. Can anyone tell me if this is actually safe, I feel it is, but I am looking for opinions other than my own, who are also knowledeable in this area.