The effect I'm after in the flanger is all about sweeping the delay time. Hence why I'm using LFO.
That's what a flanger normally does. Delay time sets the minimum time and depth sets how much the block's LFO can increase delay time.
Are you trying to create a custom smooth/stepped sweep via modifier damping and LFO quantize?
If you still want to use a control menu LFO and have control of start phase you need to choose the LFO 1B as "source" at the modifier window with the dot/graph.