Damon, just in the SBTS School of Theology, I found PhD's and post-doctoral studies from the following top-tier institutions: University of Basel, Johns Hopkins, Emory, Vanderbilt, Univ. of Toronto, Univ. Cambridge, Columbia, St. Andrews, Univ. Chicago, Princeton TS, Tübingen.
So, I don't think there's any deep bias against secular schools. Now, the point is simple. Nobody can guarantee a job upon graduation, but if you go to a top-tier school, you have a much better chance. The top programs have 70%+ of their grads in tenure-track positions within a few years of graduation. I'd like to know those statistics for SBTS or WTS or TEDS - I suspect they are far lower. Further, if you have a degree from a top-tier institution, you have a much wider potential base of employment. If you go to SBTS for a PhD, only SBTS or one of its sister schools will hire you. That's a tremendously small pool for such a packed job market.
The funding is the other thing. I'm getting a full scholarship plus a generous stipend just to go to school and be a research assistant. That means that I have much more time and energy to devote to my research than do the guys at evangelical seminaries, who are paying 10-30K per year and working on the side. The difference in quality is not hard to spot.
Anyone who wants to get a PhD is insane, unless they are independently wealthy. But some choices are more insane than others. Paying your way through an evangelical seminary to get a second-rate degree with poor job prospects is incredibly insane.
By the way, my church history professor, who has taught in Christian colleges and seminaries for over 4 decades, made me promise not to go to a seminary for my PhD.