Have I come across this type of improper install? YES.
Is it wrong? Hell, YES.
Furnaces and hot water tanks must be hard piped in Chicago. Pipe has to come to the wall behind the stove and then the stove fed with a flex line. Flex line can't run through walls or floors.
Gate valve? Gate valves are not generally approved for gas that I am aware of. Gas uses ballcocks.
You stated 'yellow flex line'. Do you mean the Pex type gas line material or a bunch of appliance connector lines coupled together to make up 20'?
From what you say the install doesn't sound proper or safe.

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Accurate Inspections & Consulting, Inc.
773/844-4AIC
Markus Keller