I never play with projection disks but I bought a couple a few years ago because I thought I might someday.  So I went back and loaded the 2007 projection disk and generated computer MPs, both with the organizaiton-wide Tools menu command and with an individual team on its lineup screen.  In both cases there were no start percentages shown for any backups.  And that is doubly odd since I'm pretty sure the disk came loaded with start percentages for quite a few backups.

I can't think of any reason why the game program would distinguish between projection disks and others when choosing whether to input start percentages.

However, even if the program did handle projection disks the same way it handles other season disks, I think your basic premise (that the CM would be more free to choose  the better player in match playing time mode when the differences in PAs are smaller) is incorrect.  Consider the following two pairs of players who play the same position:

Smith   550 PAs
Jones    50 PAs

White   325 PAs
Brown  275 PAs

Assuming Smith and Jones were the only two players rated at a position on the  team, the way I interpret match playing time is that the CM would start Smith and enter an 8% start percentag for Jones.

Assuming White and Brown were the only two players rated at a position, I doubt the CM gets to decide which one is better and go with that player.  Instead, I assume the CM start White and enter a start percentage of 46% for Brown.

And if your draft league team has two full-time players, both with 600 PAs, the CM would start each of them 50% of the time just as if you had two players that each had 50 PAs.