There are multiple ways to "depend", so if pandoc executes some external tool all of the work then might as well use that external tool directly. You will get more control over how the conversion happens, know for what search for when in trouble etc.
Sure, I don't mean that anyone would look at the Latex in between. I'm just saying that if tool x directly calls tool y to do the job then might as well use tool y directly.
Since hammers and nails are a common tool-workpiece example…consider the nail gun.
Theoretically you can drive nails with a 22 caliber blank cartridge without making the “call” through a nail gun. But you won’t finish laying shingles as quickly and easily…
Or to put it another way, there’s a reason assemblers are almost always better than machine code and compilers are almost always better than assemblers for the ends people care about.
I mean why use Latex at all when you could write your own typesetting language? Maybe because you are not a knuth.
You're confusing wrappers with alternatives. The comparison is more like if somebody published a script called html-to-pdf.sh which directly calls, e.g, chrome, would you want to use this script or use chrome directly? I would prefer the latter because (1) I would know what actually does the conversion, (2) I would know what to search for on the web should I need to tweak the output. This knowledge gives me more power as I know the actual converter. The wrapper script perhaps only helps with what the command line should be.