Don't know what you're being sarcastic about given your challenging-to-interpret spelling and grammar is making your questions difficult to grasp some of the time.
The majority of bolt-in cages still mount onto sqaure box sections which are welded onto the chassis, just like a fully welded-in cage. This is to give your cage a secure "base" to attach to, makes it easier to remove and much easier to fit in the first place. If you're not going to mount the cage on box sections (I suppose the idea is to retain as much of an OEM look as possible hence you're wanting to keep the interior) then I guess the next best thing is to mount them as you would a 3/4/5 point harness: namely a big high-tensile bolt going through your cage, through a backing plate, through the chassis and through a second backing plate. The backing plates are essential to spread the load over a large area, reducing the force on the chassis meaning a stiffer and stronger joint. Backing plates by nature, if they're made to a suitable size and shape, should be enough to keep the water out. However if you are worried then you can use anything that's water-tight really, maybe surround the backing plate with some exhaust repair gum (waterproof, heatproof and most claim to be permanent) if you've got some lying around?
For sealing the holes should you ever take the cage out - again using welded in box sections as a base avoids this issue. However if you want to skip these just use some rubber gromets from Halfords or B&Q etc. Personally to stop the grommets falling out I'd stick one in each side of the hole and put a small nut & bolt through them.
Also use stainless steel nuts/bolts/backing plates as these will not corrode.
I know that ended up uneccessarily long, sorry.
