Microsoft
Microsoft#1 - You can run the Guided Scenario as many times as you want and should have no impact provided you ensure that you assign a different AAD group (not a previously used one in a Boot Guided Scenario) every time you run a Guided Scenario.
#2 - The Guided Scenario ties multiple things together and makes it easier to assign everything together on a device group (a.k.a AAD group). You can still configure everything without the guided scenario and also configure additional things as per your requirement.
In the Intune portal,
Home > Devices > Configuration Profiles - should show all the profiles that you created otherwise or were created as part of the Guided Scenario.
Home > Devices > Update rings for Windows 10 and later - should show all the Windows Update configurations that you would have created otherwise or were created as part of the Guided Scenario.
Home > Endpoint security > Security baselines > Security baselines for Windows 10 and later - would show the list of security baseline profiles you would have created. You could have applied these profiles as part of the Guided Scenario for securing your Windows 365 Boot endpoint.