You’re correct—the rule is still being clamped by Flux’s 0.40 mm system minimum, so my verification was insufficient. I’ll correct the actual minimum/default source and confirm the computed via diameter, not just the requested rule value.

Corrected. The actual computed via geometry now reads:

The issue was Flux’s separate minSizeX and minSizeY defaults clamping the pad to 0.40 mm. Those exact constraints are now overridden project-wide.

I’ll inspect which component owns pin D3, its net assignment, pad geometry, layer, and whether an existing route or rule is making it non-selectable.

U1 pin D3 is DVSS, but it currently has no net assignment in the schematic. The project’s GND net includes U2/U3 and passives, but not U1:DVSS::D3.

Flux cannot start a PCB route from a pad without an assigned net. In the schematic:

Also remove any No Connect marker on DVSS if one is present.