If one secondary output is voltage controlled by using local feedback then, by laws of induction (Faraday), the other secondary windings will remain regulated by the ratio of their turns ratio to the regulated winding.
This happens whether in DCM or CCM. Transformer rules still apply.
However, under load, non-directly controlled secondary windings will suffer from worsening "regulation" when under load. For instance, if more current is taken on the main secondary, to compensate any voltage droop, the duty cycle will slightly increase and, this will induce slightly higher voltage on the other secondaries.
And, it's a similar story if load currents are reduced.
Is there any method to stabilize all output voltages in DCM mode?
I believe you are over-thinking the problem and convincing yourself that DCM is somehow a problematic special case.