Got an email about this, from Fabio Henrique C. Capeleiro (who also discovered the 'select keyboard' fix for FA's PMC 3d editor)from way down south in Brasil, and here is what he said:
"I discovered a way to do the planes get under the 1000 ft limit. To do this you must edit the .m files. Here's a example: Find the waypoint you wish to edit (to indentify the waypoint more easily, name it) [Altitudes are indicated by the BOLD text]
waypoint2
6
w_index 0
w_flags $1
w_goal 0
w_next 0
w_pos2 0 0 611242 10000 746057
w_speed 0
w_wng 0 0 0 0
w_react $0 $0 $0
w_searchDist 0
w_preferredTargetId2 $0
w_name _Attack SAM_
Then you change this: [yellow highlighted red text
waypoint2
6
w_index 0
w_flags $1
w_goal 0
w_next 0
w_pos2 0 0 611242 10000
746057
w_speed 0
w_wng 0 0 0 0
w_react $0 $0 $0
w_searchDist 0
w_preferredTargetId2 $0
w_name __
to 200 or anything else under 1000:
waypoint2
6
w_index 0
w_flags $1
w_goal 0
w_next 0
w_pos2 0 0 611242 200 746057
w_speed 0
w_wng 0 0 0 0
w_react $0 $0 $0
w_searchDist 0
w_preferredTargetId2 $0
w_name __
And then the autopilot will hold the altitude to even 1ft! The only problem is: your wingman can't get so low."
Wrench Note: I've been experimenting with this and discovered a few things. The autopilot WILL hold the altitude, but the cockpit voice will say 'descend to angles 0'. And if you set another waypoint, say from 200 to 500 feet, it will say 'climb to angles 0'. Which would be ok, flying over the Dead Sea or Death Valley! Just don't let it throw you; my opinion is that the games AI can't 'see' any altitudes between 1000 feet and ground level.