1. Real PCB have trapezoidal rather than rectangular trace shape due to etch process. Simulation tools should be aware of and provide an etch factor or separate width parameters. AppCad apparently doesn't, the results for 5 mils gap can't be expected to match final PCB impedance well.
Even if trace shape is modelled correctly, gap width near technology minimum for 1 oz copper will vary considerably in production. Therefore wider trace + gap can be expected to give better matching in production.
Generally, it's important to realize the limititations of designed impedance compared to impedance controlled PCB production. The latter involves test structures in PCB, sample impedance measurement and parameter tuning during production. Expect at least +/- 10 % variation of designed impedance.
2. Extreme W/H ratios will reduce the accuracy of simplified impedance calculation methods used by most tools, surely it must not be 1.0 specifically
3. Not particularly. If you want RF performance, you'll chose RF PCB substrate rather than FR-4.
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