, I agree with i3inary, cheaper, less parts to break or screw up. I have something similar in mine, and they work great.
1-The humidity dome isn't necessary. I live in a very arid place, LOW humidity, I just cut em off and stick em in there. 7-10 days later, roots, and the clone looks just like it did when it was cut.
2- Not needed.
3- I considered it, but then again, the pump heats the water perfectly, to between 72-77 degrees F. The pump also supports the PVC manifold, so you would have to create some kind of mounting for the manifold. And, the in/out would just be another area to leak, IMO. All the more reason to go internal on the pump.
4- EZ Clone has been known to over do it just a tad, especially on the 60 site.