When an X-Com craft is in flight there is no way to set the preferred altitude for that craft. (As far as I know.)
I believe that as long as the maxAltitude: is in its default -1 setting that altitude is mostly cosmetic for X-Com craft.
(Unless I'm mistaken this variable defines the height a craft can engage UFOs at, not its default altitude while flying.)
If possible I would like to be able to specify the default altitude an X-Com craft is flying at after launching.
This could be useful for example if a mod has X-Com craft that act as satellites and wants them to always display "Very High".
Alternatively the real altitude of the X-Com craft itself doesn't have to change and the craft's current altitude could be replaced by the contents of a STR attached to that craft's code in the .rul file.
For example a X-Com craft that had a line of code referencing STR_CRAFT_ALTITUDE_SPACE: "Space" would display "Altitude>Space" when ever the player looked at the X-Com craft's status screen on the geoscape, even if the craft was in reality actually at the altitude of "Very Low".