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It may be better to build the bases into the side panel itself and then use the tops to retain the switches, that way you don't need to modify the stem lengths. Unfortunately I used fucking finger painting CAD (sketchup) so I don't have fusion files of the bases you could intergrate, but they aren't super complicated to just reverse engineer the stl dimensions.

On my super hornet throttle I have all the hat switches sit very proud with a round base. (can be seen on the pyramid switch)

I don't know if the F-14 grip is the same way. Also I think my washboard switch (STEM_2WAY_ROCKER_5_WASHBOARD.stl) is too wide to fit inside the vertical switch protectors, I just eyeballed almost all the switch dimensions so I must have guessed to large

The main drawback of that though is the panel itself then restricts the kind of switch base, (2 way, 3 way, 4 way 8 way pov etc)