Flynn the Elder’s tweet mentioned “[Hillary’s] Sex Crimes w Children” but, no, might not have been about Pizza-Gate specifically. Flynn the Junior’s tweet, OTOH, did mention PizzaGate specifically.
In any event, with or without the specific Pizzeria connection the idea that this heinous liar and fool, who has called Islam a “cancer,” will be the U.S. National Security Adviser — the very important post held by such luminaries as Henry Kissinger, McGeorge Bundy, Zbigniew Brzezinski etc. — should make all sentient Americans want to vomit.
It most certainly is about the crackpot conspiracy theory connecting Clinton to an fantasized “pedophilia ring”. The distinction without a difference you are raising is equivalent to quibbling that it’s unfair to laugh at someone for believing that the moon landings were faked in the Arizona desert when in fact he believes that the fakery occurred in New Mexico.
Except the Trump campaign has now stated that Flynn Jr is no longer part of the transition team, so either Pence was lying, out of the loop, or playing a semantics game (Oh, he had a transition team email address, but he was only helping his father out and wasn’t an official member of the transition team.)