Only covers US W-2 labor. So perhaps that’s why. If only X% of labor force is elligeable and Y% of your FTE base is devs and Z% of their time is legitimate incremental novel work (defending one of those audits requires pulling GitHub/Jira/technical documentation support) then $11M is perhaps a reasonable number. YRMV.
I think it's less about the split between W2 FTEs and contractors, and instead that the R&D credits were likey government/state grants for high-tech innovation that helped to offset R&D costs, but Squarespace didn't really expand on this in their S-1.