First, if you are updating an Inovelli switch, I don't have any, so I don't know the type of their firmware file. I have only used the "first" (or original) version discussed below, to update my ZEN16.
Second, as you correctly see, there are two versions of the firmware updater. Neither type supports devices paired securely (S2). They were never updated to change the Z-Wave calls to the ones needed to support secure pairing. From the author of both versions:
Third, regarding which version to use, it depends on the type of the file:
The "original version" is the version linked to in the first post of this thread here:
Then, in order to support a new Inovelli product that had binary firmware OTA files, and that had multiple targets on the device, Brian Copeland made a quick and dirty change to the firmware updater to create the "Binary Firmware Updater". Unfortunately, the file name remained the same and the version remained the same. The link to that second version is here:
Both of these versions are unsupported now that Brian is on Hubitat staff, and will probably never be updated to support secure pairing and merged to be a single driver that fixes the bugs in the binary version and that supports all the formats in a single driver.
And finally (fourth), the upcoming 2.2.4 Hubitat firmware update (real soon now, perhaps a matter of days) includes, built-in, a firmware updater app (I am not a beta tester; I saw this in the recent Hubitat Live video). Initially it only supports Z-Wave, but, apparently, will also eventually support Zigbee (from Brian's comments in these forums). That upcoming version should have the bugs fixed and support all of the file formats. You might just want to wait for the 2.2.4 update.
Hope this helps.