I am stuck in the mode that confessions should uphold scripture. You are quite right to place scripture above confessions. The fathers may have erred.
Scripture provides only limited information on "how" and "why" there are vessels of wrath and vessels of mercy (Romans 9:11, 22, 23). But we do know God uses instrumental means to deliver the vessels of mercy (Romans 10:17). What would prevent God from using generational means to accomplish what He determined before the foundation of world (Eph 1:4, 11)?
Of course, generational means are specifically excluded in the case of elect angels (Matt. 22:30).