I did my MDIV at Truett and have just started my PhD in the religion dept at Baylor, so I think I can answer some of your questions.
Honestly, I think Baylor Religion is phasing out the MA. I would ask the admissions office to be sure, but pretty much the entire dept centers on the PhD students. So even if they did let you do that track, I'm not sure if you would get the attention you may need. Of course, if you wanted to come to Baylor for your PhD then it may give you a boost.
Truett is a very different place and has almost no institutional or faculty affiliation with the Religion Dept. Its even on the other side of campus! Its nothing like what you have at Duke or Chicago where the div school is closely affiliated. The faculties are completely different, though many of them are friends and colleagues. Truett is also very different theologically. Truett is a very protestant place with deep baptist roots and a largely pietistic student body (intuition and spirituality is prized over logical rigor and argument). Its' heavy on scriptural study (its strongest asset) and light on philosophical method or ethics, though that is rapidly changing with a couple of recent hires. It has strong historical theology and missiology folks who occasionally do something 'systematic', but since the main goal is to train pastors, the academic preparation has to be sought out on your own. You wont come out of Truett perfectly ready to apply to PhD work without having taken the time while you are there to purposefully take steps in that direction. There is no thesis/academic track really. I took 5 courses in the Baylor religion dept for credit at Truett, which helped me get a lay of the current academic land. Two of my 3 recs came from Baylor Religion and not Truett. I know a number of former truett students in great PhD programs, but they had to work more than the degree required for graduation in order be competitive. This is not a criticism though. Truett is a wonderful place. But its goals are more ecclesial and less academia.
Baylor Religion is very Duke School oriented in almost every way. There is a very strong Duke contingent at Baylor (3 grad theology faculty did PhD's at Duke) and many of our students have done degrees there. Many of the theology students are "Bapto-catholics" or Anabaptist and most all of them do some form of Christian Ethics (as opposed to say systematics). So there is some philosophical and theological presuppositions that you will never run into at Truett, for better or worse.
Let me know if you have questions about NT or OT and I can ask someone in those depts.
You may, in the end, simply want to try applying to the best MTS or MAR programs you can (Duke, PTS, Yale, Chicago, Notre Dame etc) because they will make the transition to PhD apps much easier.