For D1, the closest JLCPCB/LCSC option I found is SS54B: 5 A, 40 V Schottky, LCSC C360458, JLCPCB Extended Part.
However, I would not swap it blindly: the library result describes it as SMB/DO-214AA-class, but the package metadata is not an exact text match to the current D1D_SMB footprint. Electrically it is a strong replacement for the D1, but the footprint should be overlaid/verified before replacement.
No — I don’t see any current part collision/overlap issues.
I ran the PCB overlap DRC checks for overlapping copper, fills, traces, invalid layers, and missing footprints; there were no open errors or warnings. The layout summary also shows all 13 components placed on the top layer with low density and enough routing space.