The professors you mentioned was "then", but not anymore. Of course, Allison founded the seminary and Millikin went to school before MABTS as did Bickers, who was in the Mission field before MABTS was even founded. Beaman is no longer on faculty.
Just like things changing, there is not the well known and respected men today at the school as once existed. In the almost 30 years since you attended, the SBTS and MABTS have changed dramatically. Yes, there were past Prof's at MABTS I would have enjoyed learning from and some I enjoyed when at MABTS. Most have either retired or went to other schools since that time.
As for the seminaries working "with" MABTS, that is true. Forcing the Professors to belong to an SBC church? Yes, that is true. However, they are not recognized as a Southern Baptist School no more than DTS, TMS, LBTS, or other Seminaries. Yet, all four of the seminaries have friendly relationships with entities in the Southern Baptist world (though, LBTS has an official arrangement with the the conservative convention of Virginia, but they are still independent).
As for Stein and the controversy concerning Baptism. I have read some of what he has written on Baptism. I do not think Stein would argue for Baptismal Regeneration; he argues for step parallelism, which is not Baptismal Regeneration. Rather, Baptism is a part of becoming a Christian and intrinsic to the process, but not necessary (thief on the cross). Yet, I think this is radically distinct from Baptismal Regeneration where Baptism is mostly a mandate to salvation. It also is in contrast to the popular modern Baptist belief that Baptism is merely symbolic. Baptism is neither symbolic (nor is the Lord's Supper) nor fully regenerating. Yet, it is a part of becoming a Christian and has significant spiritual intentions which fully cooperates with repentance with distinct spiritual benefits. I believe his view fits with the statement made in Chapter 29 paragraph 1 of the London Baptist Confession 1689.
Finally, I do understand Stein's view and believe when SBTS investigated the issue they came to the correct conclusion. However, I also read what Spradlin wrote in the Commercial Appeal and was disgusted by his attack of a local Pastor in a public newspaper.
I will take Stein's view which has been examined by some of the top theologians in the Southern Baptist Convention (and other arenas) as being orthodox but I have a harder time with Spradlin's lambasting a local Pastor on the front page of a secular newspaper. Allison would never have resorted to such a display. Yet, Allison is no longer the President of the Seminary. For that reason alone I think has dramatically altered the seminary.