The important bit is "eventual". Right now, NaCl is CPU specific, and it is indeed fast. But making it portable may diminish the speed, it is not clear how fast PNaCl will be when it is finished, there are numerous challenges - for example, the LLVM bitcode that is shipped is very large (bitcode is much larger than object code because it contains higher-level information), and it takes time to optimize before it is run.
Supporting NaCl now when it is CPU specific, in the hopes of it fixing its problems some time in the future, is a big leap of faith.
As for PPAPI, yes, it is BSD licensed. But open source doesn't mean it is an open standard, nor does it mean it is usable without an extreme amount of engineering; for practical purposes, it isn't in its current state - it's tied to Chrome internals, and cannot just be dropped in Firefox or Opera; worse, it is constantly changing to fit Google's needs (mainly driven by NaCl and Flash) - it's a moving target with no spec.