I don't think it limits the ceiling in terms of the final score. If UConn had 44 possible points, for instance, you'd still be dividing the total number of points by the total possible. The only thing that changes slightly is that the fewer points you have (ie the fewer scholarships you have) the more magnified each mistake is. Conversely, you also have more opportunities to make mistakes.

Using the above example, let's say Wolf had been with the team first semester, eligible and earned both points. Then (assuming JCM lost 1 point for not maintaining the 2.6 GPA, as in the above example) it would be 43 out of 44 possible points instead of 41 of 42,(43/44=.9772 x 1000), or a 977 instead of a 971. You're always judged on the number of scholarships your specific program has, so docking the 'ships in theory doesn't matter, but it does magnify the impact of mistakes.