I fear I'm not going to help much here Re: the autopilot relationships but it really depends on which unit you are talking about!
For example a honeywell system as found on most Boeings (The SPZ-1 if we want to be boring!) Will engage the Wing Leveler and Yaw Damper upon engagement of the AP. The modern Smiths autopilots as fitted to Airbus and Embraer engage the Yaw damper only upon engagement of AP1 or AP2. If you switch it on via the MDCU/FMC then it will also engage the Nav hold.
Older smiths systems will engage current altitude hold, wing level, and yaw damper.
In FS you normally see the compromise solution as you describe.With YD an WL engaged as you press AP. There are other relationships based on specific unit combinations and how you activate it. But unless you are really trying to replicate an exact unit then just stick with the initial WL and YD.
Yes there are Autospoiler systems and Auto Airbrake systems which automatically deploy on landing, The BAe 146 and Fokker 100 I mentioned has these modelled. On the BAe 146 these retract automatically on reaching 40kts, on the earlier versions of the Fokker they were programmed to retract only when the aircraft actually stopped, which I think Is an inaccuracy as they retract on the real model at 35kts if my memory serves.
Any other questions? im very bored today! <G>