tec is right on his scenario, and there's probably at least a dozen more that haven't even been thought of yet that could occur, all which will be extremely time intensive in monitoring and determining intent.
Correct me if I'm wrong, but the spirit of the league is to set it up similar to a perpetual fantasy baseball league where each team has 20 keepers. Free agents signed in the preseason are not keepers - so why is it a problem if they are unassigned? Say I signed 10 offseason free agents to multiyear deals unassigned and still had 20 on my 40 man roster. Next season I will only have 20 keepers, since only 20 are allowed on the 40 man roster at R5 time, I will have to waive some of those signed players the following season, or others that I felt were valuable enough to keep in my 20 the season before.
A hard and fast rule that you can have 20 on your 40 man at the time of the R5 draft without restrictions on unassigned players, eliminates the seemingly enormous task of monitoring and determining intent of those with unassigned players. Plus it lessens the huge advantage for anyone who is able to log on right after the R5 draft is complete, as free agent signings at that time are immediate. Given the constraints of the game, I think that may be the best path.
Now, one potential loophole in what I described above is trades - two teams could trade players and stash them on unassigned, and as far as I know there's nothing automated to prevent tradebacks, so they could easily take that step as well. Preseason trading may have to be banned to make it work.