OK. So default profile means not just "default when FREDding a mission," but "default for any mission that doesn't explicitly say?" Interesting.
What if I add an optional ships.tbl flag that can set newtonian dampening on a per-ship basis? Something like
$Glide: <YES/NO>
+Use Newtonian Dampening: <YES/NO>
If not specified, the AI_Profiles value would be the default. If specified, the flag is set for that particular ship. That would also get around the problem where the "$use newtonian dampening" flag is useful for fighters that glide but messes up mission timings because of how it affects capships. Viola! Fighters can turn in glide mode without exceeding their maximum speed, and since non-fighters still use "retail" damping the mission timings remain the same. In other words, it means that mods like RealFlight which could really benefit from newtonian dampening on the fighters could work on existing mods/campaigns (including retail) without destroying all of the timings.
This is trivial to implement, so I think I'll go ahead and add something like this to my SushiGlide build.

Is there any good reason NOT to let newtonian dampening be optionally enabled/disabled on a per-ship basis?