No need to ruin a perfectly good piece of rope, unless you're into that sort of thing.
Yes, the tool only enables or disables option flags that are in the BCM. But, what those options are is part of the software in the BCM and doesn't get changed unless the software gets updated.
Chrysler did this a bit on earlier vehicles, but it really became big when the PowerNet architecture debuted in 2011. Many modules are used across trim levels and, in some cases, across models and brands. This reduces the number of different variants of modules and software and makes manufacturing easier as well. The BCM maintains the vehicle's unique configuration and it, along with the rest of the modules, use this configuration data to determine how they should behave. The radio queries it to determine what buttons to show. The lighting control uses it to know how much current a given lamp should draw (LED vs incandescent) and so-on.
A configuration file is loaded at manufacturing and this is what populated all the option flags in the BCM. The official way to change them after the fact (as we know) is to update the build for that VIN in FCA's system and download a new configuration file. When you use other tools to modify the option flags directly, things are less automated. But, you get to the same place. The most important part is that you're not at the mercy of what FCA chooses to let you change.
Some of the downsides are that everything will have to be done again if the dealer ever restores the truck with the "official" configuration. There's also a bit more guesswork involved. While the dealer might be able to add a single code for the LED taillights, this doesn't translate 1:1. The BCM options are meant to not be specific to a particular vehicle, so they have more granularity. On the trucks, LED tails would require the BCM to have the LED option set for rear parking, rear turn signal, and stop lamps.
So, it's not a simple plug and play thing for the average user. If you're not careful you can turn your truck into a boat anchor. But, it is the best option we have and it works. The upside to this granularity is that we can set things that out trucks never supported from the factory, like keeping the fogs on with the highs. Or LED reverse lights, or HID headlights.