Perhaps they decided to separate because the Scriptures demand, although sometimes that demand is seen by some sooner then others.
An example may be the decision of no longer endorsing Billy Graham.
Some recognized the chase to embrace modernism much earlier then others. But ultimately those who were theologically sound had issues with him.
They may not have separated, but neither were they wildly enthusiastic.
Please reference my paper "Has Fundamentalism Lost the Gospel" at Has Fundamentalism Lost the Gospel? on the BB. I think you will find it very interesting and will add to your thoughts here on this thread.
I actually do have a favorable opinion toward secondary separation, but know the human nature more often used it for self positional authority then a matter of purity in truth.
Unfortunately, because it got such inappropriate exercise by some who had agenda driven rather then purity driven issues, the backlash has destroyed much of the truthful reasons for such a separation to be in place.
As a result (imo) confusion and lack of discernment has inflicted the assembly so folks are much more inclined to fellowship and include that which is questionable.