If that was the case they could have shipped IME-free machines from the start. They are selling whitebox machines for an exorbitant markup with their own spin on a Linux distro.
Disabling IME can have other impacts, and Purism even has a blog post explaining what the issues were and how they resolved them -- once they figured out what IME modules were needed for their laptop to work properly they could disable IME with a software update.
I don't know if that's how they did it, but you're misunderstanding the difference between disabling IME and enabling internal flashing.