There is a problem with transitioning planes. It is probably due some another mod installed, but I cannot target which one. Anyway I think that creating new plane and copying everything from old plane is not best aproach - actually, not everything was copied. As I understand it is only for making airborne plane with/without collisions. Is it really no other possibility, like changing collision flag after creating item or just ignoring collisions after plane take off?

The mod Aircraft Realism (2.0.3) caused a non-recoverable error.
Please report this error to the mod author.

Error while running event AircraftRealism::on_tick (ID 0)
AircraftRealism/logic/planeController.lua:61: Old plane and new plane inventories are different sizes. Check plane prototypes
stack traceback:
[C]: in function 'assert'
AircraftRealism/logic/planeController.lua:61: in function 'copyInventory'
AircraftRealism/logic/planeController.lua:230: in function 'transitionPlane'
AircraftRealism/logic/planeController.lua:470: in function 'checkTransitionTakeoff'
AircraftRealism/logic/planeController.lua:482: in function 'updateGroundedPlane'
AircraftRealism/logic/planeController.lua:547: in function 'handler'
AircraftRealism/control.lua:48: in function <AircraftRealism/control.lua:40>

List of mods:
base, aai-containers, aai-industry, aai-programmable-structures, aai-programmable-vehicles, aai-pv-crafting-group, aai-signal-transmission, aai-signals, aai-vehicles-flame-tank, aai-zones, AbandonedRuins-base, AbandonedRuins_updated_fork, Actual_Craft_Time_2, Aircraft-space-age, AircraftRealism, alien-biomes, alien-biomes-graphics, Armored-train, artillery-equality, assault-rifle, AutoDeconstruct, biter-factions-ng, Bottleneck, bullet-trails, Clockwork-2, Cold_biters, combat-mechanics-overhaul, Common-Industries, DiscoScience, dynamic-rain, EditMapSettings, ElectricTrains, EpicArtillerySounds, Evolution Reduction, Explosive_biters, factorio-crash-site, far-reach, Fill4Me, flib, Gun_Turret_Alerts, HelicopterRevival, Honk, Infinite_Combat_Robot_Lifetime, informatron, inventory-repair, invincible-construction-bots, Invulnerable_Rails, jetpack, lane-balancers, mferrari_lib, Mining-Space-Industries-II, OverloadedTrains11, Power Armor MK3, Purple_Acid_Rain, realistic-flashlight-fixed, RoboportTweaks, robot_attrition, Robot_Battery_Research2, Rocket-Silo-Construction, SchallTransportGroup, shield-projector, show-max-underground-distance, space-exploration, space-exploration-graphics, space-exploration-graphics-2, space-exploration-graphics-3, space-exploration-graphics-4, space-exploration-graphics-5, space-exploration-menu-simulations, space-exploration-postprocess, space-spidertron, spidertron-extended, squeak-through-2, TimeTools, turret-activation-delay, turret-library, visual-signals, water-is-not-infinite, ZRadar

The crash is because of AAI, it modifies the Aircraft mod (not Aircraft Realism) and changes the inventory size of the grounded and airborne versions.
When you try to takeoff Aircraft Realism notices the inventories are different and gives you that error.

Unfortunately AFAIK, the collision mask is part of the prototype and cannot be modified at runtime - hence the copying technique.