Is it feasible to modify the FPGA architecture and generate a revised XSA file for software handoff?

Kindly refer section Yocto Build Procedure from software user manual, which explains creating binaries with custom XSA (modified FPGA design) in detail.
Also make sure to review the system-user.dtsi according to your FPGA design.

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Please find the detailed product information here:
Zynq™ UltraScale+™ ZU7/ZU5/ZU4 MPSoC System on Module