I am not too worried about getting the 90-day window in for Song this year, though there is still time if they got him ready for games by the beginning of July. This year is most likely about assessing his talent and whether he is worth keeping. They might very well get him up to the major league roster for a month or two this year. Then they will probably know if the stuff is worth keeping him on the roster all winter. I don't think we have a huge number of young players we'll need to protect yet.
Worst case for the Phillies is rehabbing him all year (but deeming the stuff is good enough to keep). Then playing him for 90 days next year after Australia or Arizona in the off season. Then he still has all 3 of his options.
The Phillies know much more about where he is in his recovery and the level of his stuff than we do. They will make an informed decision on that.