The PortableApps.com launcher supports passing command-line parameters to the real chrome.exe. It also supports passing parameters on all other apps.
Here's the archive with all the different versions I was able to find. It has version 11.5, 13, 11.6, 11.4, 11.9, 12, and 16 beta. The Version.txt file in the downloaded archvie has the more exact version of Chrome that the Pepper Flash plugin came from.