Before I pulled the timing gears, I realigned the dots on both (this put the dowel in approximately the 6 o'clock position). So long as I don't move the cam during reassembly it should align correctly because of the dowel. Just have to be careful not to be off one tooth, but again as long as the cam doesn't move I'm okay. With the complete valvetrain in place there is already much friction/pressure being exerted on various cam lobes, so it's not going anywhere. I also have the battery disconnected and the ignition keys on the seat so nothing stupid happens.
EDIT: To answer your question, so long as the dowel (loose or not) was engaged with the cam gear properly, there would be no loss in timing. It would have to be very sloppy loose (i.e. a 1/4" dowel vs the 5/16" that's in there) for a timing change to occur.