I think what you’re referring to is this:
energyFrequency = {type = 'config', parameter_number = 3, size = 1},
ledIndicator = {type = 'config', parameter_number = 3, size = 1},
However that is a red herring. The profile for ge-fan-scene doesn’t contain a preference for the “energyFrequency” tag, so its ignored from the data set above. This allows multiple sets of parameters in code to match to different parameters based on the profile itself (ie, the GE_SCENE set is used for switches, dimmers and fans, and only the preferences listed in the actual profile used will map to a parameter_number, etc.)
As to your specific issue of why you can’t change the LED parameter settings on the 55258, more information is available here. The TLDR version: changing the LED operation is not supported on the 55258, either by zwave parameter nor by tap-sequence. For the future it might be helpful to do a search by model number to get any past history to help quicker.
Why have the ledIndicator parameter available on the profile used by the 55258 at all? The profiles in these consolidated drivers are fairly generic on purpose, most devices follow the same patterns of which parameters they support by generation. For whatever reason, the 55258 is an outlier and it wasn’t worth making an exception for just a single device.