CI: Refactor code related to `test_apply_config_to_edb` or strengthen CI

[SMoraisAnsys]

When running the extensions tests on Linux, it happens often that test_apply_config_to_edb fails without changes associated to this part of the code.

See https://github.com/ansys/pyaedt/actions/runs/18646749738/job/53156210783

[SMoraisAnsys]

Pinging @hui-zhou-a and @svandenb-dev for visibility

[SMoraisAnsys]

Extending this flaky marker to tests/system/extensions/test_export_layout.py::test_export_layout_all_option, see

https://github.com/ansys/pyaedt/actions/runs/18650651620/job/53168385951?pr=6789

[SMoraisAnsys]

Extending this flaky marker to tests/system/extensions/test_export_layout.py::test_export_layout_ipc_only, see

https://github.com/ansys/pyaedt/actions/runs/18681857757/job/53265428535

[SMoraisAnsys]

Extending this flaky marker to tests/system/extensions/test_export_layout.py::test_export_layout_config_only, see

https://github.com/ansys/pyaedt/actions/runs/18688682881/job/53289641692

[SMoraisAnsys]

Extending this flaky marker to tests/system/extensions/test_post_layout_design.py::test_layout_design_toolkit_microvia, see

https://github.com/ansys/pyaedt/actions/runs/18707742802/job/53349586488