Quick access cap indeed has to be removed if you want to use the Knee Neo Lever. You're going to be able to move the stick, but you can feel it scratching the cap which is not ideal. Source: have the same board and tested the IST knee lever and Knee Neo lever
Depends on the lever. Levers with no collars can fit, short collars can mostly fit. Full collar levers won't fit without heavy mods. Some short collars won't work like the Fujin V3 with the short collar mod. The new Samduska Crown Knee Neo and Shinsun won't fit due to height of the body (maybe the gate has something to do with it too). Probably the Infiltration lever won't fit either. Eclipless shafts with the bolt/screw won't fit properly unless you shave down the bottom of the FS Alpha case under the shaft. Anything attached with the BitbangGaming Shuriken PCB (both V1 and V2) won't fit in the FS Alpha.