This isn't about what makes sense. This is about finding a punchy number that sounds big and makes Trump's base happy. "$100k fee (that covers 3/6 years)" sounds more impressive than "$33k per year" or "$17k per year", so that's what they went with.

Ultimately this isn't going to do anything to reform the H-1B program; this is just trump "doing something", which he'll claim as a success (and his base will eat up), even if it does nothing or makes things worse.