There are also ways to roll on urethane coating, which ends up looking cool but there are plenty of issues with it. Among them, the prep work is tricky but important, the urethane is expensive, and on a really hot day it can even stick to itself if you roll the boat up. Not fun.
To answer your first question, with many brands of boats built from more stretchy fabric, you would want to lay the actual chafers down with the raft deflated for sure. An Achilles, for example. But this AIRE material has so little stretch it is better to do it fully inflated, to at least a solid 3 p.s.i. in the tubes - maybe even a bit more.
The best thing to do is get MEK (not the new fake MEK-substitute), wash one side of the wear patches and area on the boat where it will go, then put the lid back on but keep the MEK can handy. Always use cotton rags, never anything made of nylon - it will melt. Then lay the chafers down & trace the outlines with a pencil. Use masking tape or whatever tape you can find that will stick well, and mask of the outline. Leave an 1/8" or so all the way around.
Get some 2" or 2-1/2" wide throw-away grade brushes, cut the bristles to 1", and put on a thin coat on both chafers and both areas on the tube tops. Let it dry a minimum of 45 minutes, but up to overnight is probably okay. We usually go an hour to 90 minutes. The reason for cutting the brush bristles is that it allows you to spread the glue thin more easily, and larger sizes like 2" let you work way faster than a 1" brush would.
Once that's dry, go back and quickly put a second coat on just one chafer and one side of the boat. Let this second coat dry 10 minutes. Now check and see if the chafer will bond to the area on the boat. It shouldn't unless it's very cold or humid the day you are working. (if it still seems tacky wait another 3 to 5 minutes). With the chafer laid down & lined up in position lift up about a foot or so at one end, get your rag again, wet it with MEK, and wipe the foot of chafer and matching area on the boat. After about 5 to 10 seconds it is ready to lay down. The MEK re-activates the glue. Fake MEK may not work for this purpose, and could even contaminate the glue. I'm not sure to be honest since we have no experience with it, but I would not chance using "MEK substitute".
Now lift the chafer from the other end, and wet another foot, lay it down, and repeat until you get to the far end. Then repeat all this with frame strip #2. Having a second person might be helpful.
Use a putty knife (with the corners rounded a tad and the edges sanded a little) to burnish the patches. The narrow edge exerts far more force per square inch than a rubber roller, and a skinny metal roller tool would take all week to cover every square inch of those chafers.
When you burnish with the putty knife, work from the center (cross ways) out to the edge. Do not burnish the long way along the six foot length of the chafer, because you can push a wrinkle into the chafer doing this.
Let the glue cure overnight and you should be ready for action.
Maybe using some 303 Protectant on your boat might extend the pvc's lifespan a bit too. For what it's worth, my family has a 5-1/2 year old pvc pool cover that is still functional, though the material is not as flexy as when it was new. Then again, it's made with Heywinkle (German) pvc, which is not as high a grade as the French Ferrari fabric your boat is built from.
It sounds like your boat may now be out of warranty, but even if it wasn't I can tell you for certain chafe patches or extra D-rings will not void AIRE's warranty. This is not to say other "modifications" won't though. Things like punching extra bail holes in a kayak definitely will void it.