I have never removed the boot but I filled it with silicone dielectric grease to fill the void to help dissuade moisture ingress. I haven't the foggiest idea if it makes any difference or not but my SMC is still the original from 2009 and it still works as it should.
There's nothing wrong with removing the boot to do that - although the boot itself makes a perfectly adequate seal if it is not disturbed. The problem is that if the boot is pulled out, the 'brim' of the top hat shape does not seal by itself when it is replaced. It requires some effort.
The image below is taken from a more detailed explanation
here.
The problem is getting the brim of the top hat pushed in beyond that angled step. It wants to rest in the wider part of the bore and feels as though it will not go any further. I found a driver from my socket set which would fit inside the alloy opening and the top hat rubber boot would fit inside.
You are pushing a sprung circlip into a hole that is too small for it. The angle on the face of that hole - the angled step - is just about enough to squeeze the circlip into a smaller shape. Imagine doing that with the circlip in hand with fingers. The angled step will squeeze the clip to the right size, but it requires a hefty shove. A bit of silicone grease will help around the brim. You cannot mistake it when you feel it push into place. But you can convince yourself that it is fitted properly when it isn't.
I undid the bracket - the one that you are not supposed to undo - in order to do this. I measured the length first. Funny how you are not supposed to undo it, but it has instructions to apply thread lock and gives a torque value !!
I keep meaning to find some tubing of the correct diameter and cut it to length and saw it vertically in half so that I can wrap it round the top hat and use that to push the brim into place. A bit like fork seal drivers. I'll do it if I ever need to remove the piston again.
Photo is the pre-2008 version.
It is important because if water gets past that boot, the air side of the matser cyclinder is open to air and water - it can get through the hole int he washer through which the push rod passes. Once in there it can corrode the bore, which stops the piston from returning properly and that serious rear brake lockup due to the piston not being able to move past the tiny compensation port.
More silicone grease inside may help a little bit, but its not going to stop it.
The drain hole is to get rid of any rain water pooling around the brim. I guess that if you can poke a soft probe through that drain hole (pre-2008) and see it from the plunger bracket end - then the boot is in the right position. If the probe meets the rubber, then it isn't.