Well, Autofill is meant to shorten queue times by dropping players into an unspecified role - so, my guess is, it spends some time looking for groups with your Primary or Secondary pick open, and after enough time spent (I'd hazard to say around 2m, 30s~, maybe 3m~) - it starts searching for groups with any openings.
So far, it's been exceedingly rare for me to get autofilled - so I'd assume that even with Autofill active, the matchmaking queue still prioritizes your Primary and Secondary, at least for the first few minutes, after which it prioritizes getting you into a match over your lane choice.