One smart aleck but serious question - what precisely makes the naive scientific distinctions wrong compared to the philsophical argument? It is overly literal

One smart aleck but serious question - what precisely makes the naive scientific distinctions wrong compared to the philsophical argument? It is overly literal and somewhat unimaginative to immediately answer theship of Theseus with "Did it sink or wind up disassembled in whole? If not then it is the same ship." But it is a consistent philosophical framework - it never was destroyed so therefore it is the same ship. Is it convention and semantic akin to say "literally" being used as figuratively? While clearly bad for cross communication and a reciepe for confusion self-consitency is all that is needed for within subset communication even if it leads to cringeworthy constructs like "he actually literally exploded" for what was previously just "he literally exploded".