Pagetest (the underlying code, not the web UI) supports a fairly rich scripting interface. The documentation for it is available here: http://sourceforge.net/apps/mediawiki/pagetest/index.php?title=Scripting and we use it extensively for testing things like mail, shopping, search and other multi-step transactions.
WebPagetest offers a reduced capability where the full scripting language is available but it can only record the performance information, screen shots and video from one of the steps. The documentation for it is available here: http://sourceforge.net/apps/mediawiki/pagetest/index.php?title=Hosted_Scripting.
The main reason the hosted version doesn’t support multi-step transactions is that I haven’t figured out how to present the results in the UI (particularly if you are doing more than 1 run). I do have a ticket open to implement it but it hasn’t bubbled up to the top yet: http://dev.webpagetest.org/pagetest/ticket/16