I added a lead late in a campaign and wanted to send him some content instantly, so I used the single email flow option as described in http://community.marketo.com/MarketoArticle?id=kA050000000LA1UCAW
Is there any way to track opens/clicks/lead scoring with this method? I now know that a better way would be to simply run the campaign again, excluding those who had received it before, but it'd be nice to retrospectively apply scoring at least.
Either way, yes, Marketo tracks opens and clicks regardless of how you've sent the email.
If you want to move the Lead into a Program and have Progressions, all you need to do is run a single flow action like:
if you want, you can then run a Change Progression for Opens, but Open is always before Clicked and so you should run this first or not at all because you can't make a Lead go backward in the Progression.
Change Progression: Choice 1: if Clicked Link In Email IS "Email 1" then Progression IS "Clicked Link" Choice 2: Do nothing