I can tell you from my experience that the boot/tube is better than the completely encapsulated strip. When you are done, just use hot glue to cover the ends and splices. I'll suggest that you might consider sealed modules instead - that strip while good, isn't intended to be used like strings of Christmas lights - they'll break pretty quick.
The waterproof by epoxy coating gives out better light, so i have been told, but at the same time its very difficult to cut and join due to the resin.
The silicon tubing is very easy to work with, cut and rejoin and I'm happy with the light appearance. The CCR from LOR are made with the silicon tubing and I have cut a few of these up and rejoined with great ease. Just use a bit of silicon to reseal them up.
Now the best method i believe to mount the strip would be to use electrical conduit as its cheap and mount it to that. put a few hooks onto the conduit and then you have a quick and easy way to mount and remove your lights from your gutters. Also do the same with your windows and make a frame out of conduit, this way you should not damage your strip.
So in the end i would recommend the silicon tubing as it is so easy to work with and the light appears to be great anyway.
As an add on to FE's response - another method to mount it is to purchase "L" shaped roofing drip-edge. Just get some 3M Super-90 and glue the strip to the edging. The edging is galvanized so it won't rust and you can attach it in a variet of ways to the gutter/shingles.
Here is an item I made out of about 6 meters of 5050 60 LEDs/m silicone booted strip: