The choice of countries actually dates back to a 2015 Act of Congress restricting access to the Visa Waiver Program to nationals or prior recent visitors of certain countries. These people will have had to apply for a visa instead, and presumably are subject to more stringent checking than most.

The list of countries wasn't defined by Congress beyond Iraq and Syria (presumably thanks to those being specifically called out in the name "Islamic State of Iraq and Syria"). It did include provision for the Secretaries of State and Homeland Security to designate additional countries.

My gut feeling is that the current administration didn't choose to target the same countries deliberately, but rather chose to incorporate the prior legislation by reference as a defence against legal challenges.

The EO wording is that "immigrant and nonimmigrant entry into the United States of aliens from countries referred to in section 217(a)(12) of the INA, 8 U.S.C. 1187(a)(12), would be detrimental to the interests of the United States". The referenced legislation is here: https://www.law.cornell.edu/uscode/text/8/1187#a_12 .