Is the introduction lesson now considered one of the lessons to make a total of 48, or is there some other design here? I simply would like to know so that if I am asked to propose the schedule in light of this situation, I will be able to address it. If they never ask, I'll just be happy that it's been done, even if it's not quite how I would've done it.

Oh, my basic understanding of how it's supposed to work is two lessons per month on the second and third, and the exceptions in the individual wards will work around the rule. If there were 24 (or 48) I would assume lessons 1 and 2 for January, 3 and 4 for February, etc. This way the Stake (and likely the Church) is unified in which lessons are being taught which weeks, and unfortunately some of the lessons just don't make it in when a ward has a conflict.
Thanks for any feedback you might have.