Both the visual and the audio warning for fire are way too inconspicuous and can be missed very easily when faced with a lot of other indications that come with an engine failure. So it's a scenario that a fire indication was not recognized and fuel not shut off.
On the other hand I don't think it's "abundantly clear" that the crew was unaware of the fire, based on the communication with the tower only.
According to googled images N109BC seems to have had the hole in the cowl aft of the battery door. The hole that's there in order to read the fire bottle pressure indicator. I don't know if that hole is always there or only on machines equipped with the fire suppression kit.