A motion by the court to dismiss all plaintiff's claims " with prejudice" AFTER a settlement had been reached by the parties would indicate a greater possibility of a satisfactory settlement for the plaintiff than a court ordered dismissal of " with prejudice" before a settlement had been reached.
While the above statement is certainly correct, it seems that you're comparing apples and oranges. The latter part, i.e., "...a court ordered dismissal 'with prejudice' before a settlement had been reached", would be indicative of no settlement at all --- in that scenario, the plaintiff would have won the case outright.
As to the question I think you're really asking, there are lots of reasons for "with prejudice" versus "without prejudice" dismissals. While there are certainly exceptions, the effect of one as opposed to the other is most often a formality and has little substantive effect on the case. As a result, it really isn't possible to validly conclude that a settlement was more favorable to one side or the other based solely on whether it was done on a "with" or "without" prejudice basis.
Hope this helps. Let me know if you have further questions.