Hybrid Boost-Flyback Stability Issue
For anyone interested, the issue turned out to be layout related.
It seems the feedback signal was such a high impedance, with the most sensitive part running near the transformer, noise was coupling into the system and being amplified.

There is an effective ~100x amplification of noise after the high voltage divider created by R9,10 &amp; TM1 on the output.

The high voltage divider was made with lower value components and moved closer to the LM3478 IC, and the issue has disappeared as well as there is overall better stability on load shifts. At the cost of dissipating way more power.