A work around might be to get the tourney started and then add another table call it say "Alternate list" and make it the size of the number of alternates you have. Then buy in and seat the alternates at that table in the order of which they are to be added. I.e. 100seats available, 105 people show up, Alan was 101, Barry was 102, John was 103, Steve was 104 & Tim was 105.
Set up a new table called "Alternate list"
Add Alan (dont buy him in though)
Seat him at seat 1 on the alternate list table (drag and drop)
Add Barry (dont buy him in though)
Seat him at seat 2 on the alternate list table
etc
Now when a seat becomes available, you simply buy in alan and drag him to the table & seat which is open, you then still have your list of alternates.
I tried this just a minute ago and it does not affect the Average stack, total chips in play etc.
I hope this helps
Regards
Ian