@ChiChiWerx @GINGER01 @Shmexysmpilot Thanks!

Alternatively, you could also do it with traditional XML modding, but that is highly tedious and easy to miss individual pieces and parts. Something to remember, though, there are still attributes you cannot access with Overload--the ones I know are custom colors and reflectivity which I still go through the XML file to mod. But, 99% of what I mod, I just use Overload. As for Fine Tuner, I primarily use that for angling individual parts or groups of parts.

1. Get Overload--if you're on iOS, sorry, you can't add mods to your iPhone. Once you've installed Overload (I also highly recommend Fine Tuner--you can find both mods under the "Mods" section).
2. Click on the first part of your custom landing gear--strut, rotator, wheel, whatever. It will highlight yellow.
3. Click on the Overload icon at the bottom of the screen.
4. At the top of the dialogue box, go to the "Part" dropdown submenu.
5. Next to "No Collisions", you should see "False". Delete "False" and type in "True".
6. Repeat for every landing gear part.
7. Test your landing gear--if it "glitches", gets stuck, vibrates or flutters, there's probably a part which still has No Collisions set to False.

If you have the overload mod there is a section if you click on the part that says disable collisions. If marked false the part will go through the wing.

There is an XML attribute called disablecollisions or something. If you can access the code, set that to true for any parts that need to intersect the plane. If not, there are full sets of parts with disabled collisions that users have uploaded to the site. Make the gear out of those parts and they will not collide with the plane