I'm pretty sure Boeing isn't laughing all the way to the bank right now.
I work in a regulated industry (medical) and I can assure you that I have never seen a Safety threshold that was in any way related to manufacturing or any other cost. The thresholds are always set according to how much harm can be caused and the likelihood of a harmful event.
Reliability, on the other hand, has tradeoffs relating to costs. However, in this case, an unreliable subsystem can have a clear safety impact, so its reliability directly feeds into the Hazard calculations. In other words, Safety concerns would dominate.
I hope that actually conveys what I'm trying to say. A bit rushed right now :-)
Imagine employee A delaying the trials of the "most modern aircraft in the world" because some batteries are "malfunctioning", HE SAYS SO AND IS STILL WORKING FOR US?
It is not just Boeing having a conflict of interests, it is its employees as well.