When refitting - the rubber boot is supposed to fit inside into that groove formed by the double ridge. I don't know if it is possible to do that without remove the boot first - but then you have the problem of seating the boot properly. A gentle push in on both sides simultaneously with something long thin and very blunt should do the trick.
The top of the boot is folded in on itself so the lips of the top can fit into the groove.
The brim is often sprung - either by the nature of the thick rubber, or by having a sprung wire inside. The bore into which it fits usually tapers so that the brim presses firmly onto the side to form the waterproof seal. This cannot be done with the lever in place. You might be able to find a hard tube that fits over the top so that you can press the brim into place. For the SMC boot I can use a socket from my driver set. I don't know about the clutch boot - although I have fitted one, and it wasn't a big issue.
But if it isn't pushed home, water can get in and that will present problems later on.