Yes it is okay to perch the backbone rails on top of the plastic bolt sleeves. They will compress as you tighten the bolts to secure the backbone rails to the roof.
One thing I strongly recommend is to go heavy on the butyl tape and waterproofing of the holes. One of my friends recommended this to me after she had to re-do her installation because water got into the headliner of her FJ. When I did mine I put down a double layer of tape and injected silicone into the bolt holes. It’s been five months and no evidence of leaking.
One other thing that I did was to swap out the provided channel nuts with ones that have springs on the back (they’re standard M8 by the way). On my first install attempt I had a terrible time getting the channel nuts to stay square in the channels while I started the bolts on them.
Also I mounted my rack well forward to clear the tailgate ladder so I had to raise it up to clear the roof antenna. I did so with machined aluminum spacers and stainless steel fender washers to provide a generous perch for the c-channel.
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