Alt: Altitude above MSL [Probably based on whatever you have set in below mentioned setting or always pitot-static, this is not mentioned and I haven't tested that]
AltIGC: Altitude above MSL( [based on] IGC [sensor using cockpit air pressure])
5.1.1.4 Altitude Source
The system has two pressure altitude sensors. One is built into the main display unit and is
used for the IGC recorder and the second one is built into the vario unit and is connected to
the glider pitot-static system. Changing the altitude source defines which sensor is used for
pressure altitude used in program.
Above are excerpts from the LXxxxx Manual (lx90xx-80xxUserManualEnglishVer802rev41) [with my comments in square brackets].
1. Difference between the two is stated above, normally you would want to have the altitude used to be from the pitot-static system, as this has less errors than the cockpit pressure. Depending on your cockpit ventilation you get a slight over or under pressure compared to static and this will change your AltIGC a slight bit.
2. Both Alt and AltIGC are set when powering on the instrument, actually it is the QNH that is set that way.
3. The same setting is adjusted with Settings/QNH.
4. You can choose, normally you would take pitot-static.
The IGC file records "RawIGC" and GPS-Altitude, corrections for QNH are done in post processing and might differ between platforms.
Now the question remains how the airspace infringements are calculated in the software used. But in general, yes even if you have an offset from cockpit ventilation the trace should not show an infringement if you use AltIGC.
My take on this however is to use normal Alt and calculate some extra safety margin in to allow for the difference from Alt to AltIGC, you could also test this difference in various configurations (Ventilations open and closed, sliding window open and closed, different angles of sideslip, at different airspeeds).
Benjamin Meier, SGPilatus, Switzerland