I'm not sure I see why the GUI must only be able to present one mode or the other at any given time, controlled by a setting.
Either a combined functionality window (e.g. another item in the airport class drop-down), or one window or toolbar button for each mode, would work just as well.
Ah, I think I see what you mean. But ultimately I think every patch should have the goal to get into trunk - whether it actually happens or not, and then it makes sense to be able to turn it off
Having an on/off setting is rather orthogonal to targeting future trunk inclusion. That aside I don't think that every patch should try to get into trunk, for most patches it's unrealistic and setting unreachable targets is not a good way to sustain motivation.
Even if NOT talking about trunk inclusion it makes sense for for example patch packs. You can also set daylength factors to 1, so if you download a patch pack for features x, y and z but don't want daylength you can essentially turn the patch off.
GUI issues aside, there'd be nothing stopping players from just not building the new airports, so I don't really see that an on/off setting would add much except in a multi-player environment where such features were considered undesirable for whatever reason. This is not the same as something like the daylength factor which has significant side effects even if the player takes no action.
That aside, I don't think that converting old savegames is insurmountable. If your new layout mechanism is sufficiently flexible that you can create a tile and reservation layout which closely-enough matches the old airport layouts and state machines, you can do the conversion at load time as necessary. If strict correctness isn't an issue but economy of effort is, you can also just throw all aircraft in the air at conversion time as some other airport patches do.