Follow-up work from #5113 (inject-implicit-output): disabled tests and underlying bugs

• PR #5113 (merged; 383c736f18) enabled the quantum optimizer broadly and added compiler-injected quake.log_output markers (inject-implicit-output / erase-implicit-output) so degenerate kernels are not optimized away.
• Landing it required re-enabling target .yml pipelines that Python had been silently dropping, which exposed a set of pre-existing bugs.
• Per offline discussion, several tests were disabled rather than chasing all of them. This issue captures that deferred work.

Disabled / weakened test surfaces

• python/tests/backends/test_Ionq_LocalEmulation_kernel.py
• python/tests/backends/test_Quantinuum_LocalEmulation_kernel.py
• python/tests/backends/test_Quantinuum_LocalEmulation_builder.py
• python/tests/mlir/target/cudaq_observe.py
• python/tests/mlir/compiled_module_cache.py
• test_compiler_bench_nisq.py::test_routing_inserts_swaps_on_path
• test_kernel_parameters.py::test_nested_list3_bool/int, test_nested_list4_int
• test_run_kernel.py::test_run_and_sample_and_direct_call
• quake-remote-backend-tests

Start by running the remaining unchecked tests in test_compiler_bench_nisq.py, test_kernel_parameters.py, test_run_kernel.py, and the quake-remote-backend-tests, then compare failures with PR #5113 and the listed disabled test files. Done means the deferred failures are fixed and the affected test coverage can be restored without regressions.