Just say that then? He was intentionally misleading or he was lying.
EDIT: Put another way: I'd believe those kind of whistle-blower protections are meaningful when we see these agencies admitting to past failures that have been brought up and taking proper responsibility and demonstrably taking steps to ensure better oversight. Until then, the safest assumption is that making use of any whistleblowing provisions they claim to have is at best ineffective, at worst dangerous.
https://federalnewsnetwork.com/federal-newscast/2018/12/pent...
These protections are used all the time- it just doesn't always make the news.
>demonstrably taking steps to ensure better oversight.
Like expanding the protections? We see a whistle-blower complaint right now in the news working pretty much as intended, with the whistle-blower's identity being protected.
https://en.wikipedia.org/wiki/William_Binney_(U.S._intellige...
As for the Pentagon, you'll note that part of what it covers is that the Pentagon Inspector General has struggled to substantiate allegations of retaliation in most cases, to the point where they ended up resorting to introduce a new system of mediation to resolve cases. Maybe that's because the allegations were bullshit, or maybe that's because the system is totally without teeth. In either case it does not illuminate the case of Snowden at all.