Naming no names and discussing no specific forbidden third party things, my—admittedly presently sleep-deprived—understanding is that the third-party tool in question bases it on whether the combat log is told to say "X uses Y" or "X casts Y", which indeed a very simple script. However, my understanding is also that the 'casts/uses' message is not actually based on whether the damage is magical or physical, but whether the originating ability is handled as a weaponskill or a spell.
But whether it's a weaponskill or a spell isn't guaranteed to be tied to the type of damage, but rather how it's handled in other parts of the combat system. RDM's Enchanted Moulinet, for instance, is a weaponskill (...I think?) but does unaspected magical damage, while the non-enchanted Moulinet—also a weaponskill—does physical. Because it is a weaponskill, you should still be able to use Enchanted Moulinet when silenced (provided you had enough black/white mana before getting silenced, anyway), but it will still do magical damage.
Conversely, it wouldn't surprise me if the three mobs with the obnoxious AoE paralyze in Puppets' Bunker are using a spell (since it's a cast-bar that can be interrupted), but that the attack which paralyzes might well do physical damage. (Mind you, it wouldn't surprise me if it does magical damage either, because rational definitions of magical and physical do not always apply in this combat system.)
Though whether the originating attack is a spell or weaponskill will probably get you like 95% of the way there, admittedly.
And I certainly may be wrong; I haven't bothered to try to slice open the FFXIV network protocol to know whether or not it actually does include the type of damage rather than just the indicator of whether the source is a spell or a weaponskill, nor is the source code for the totally hypothetical unnamed tool available that I know of to take a quick look at it.
However, my larger point is just that from (somewhat painful) personal experience, I know how design decisions made early in a game's life that made sense at the time can come around to bite you several years later when players want a seemingly-entirely-reasonable feature that has you tearing your hair out to try to figure out a sane way to implement without having to gut chunks of established systems to do it.
It's certainly conceivable that for some reasons Square-Enix is just making excuses and the client has all the information needed, and they could do five minutes of work to make it happen. But it's also possible that Square-Enix made some decisions years ago which became part of the scaffolding of current systems, and trying to take out and replace a piece is like trying to remove one of the bottom sticks in a Jenga tower: sure, it's possible, but you're going to live in fear of the Jenga tower falling over.