I would say that they are two different things, a collet being just a fixture for a tool of your choosing and a morse taper end mill being exactly that, a morse taper shank with a carbide tip fixed in place with a hold down screw.
You could argue that the collets are better because you can choose different sizes and tools to fit in it but with the morse taper end mill you are stuck with whatever diameter it is. Then again, if you buy it knowing you want to do alot of work with 1 particular size then maybe you would favor the cost saved by using a tipped tool at the set size, because you dont need to re sharpen it and just replace the tip. So its a matter of what you want it for.
I'm gonna go against the grain with this, but would argue theoretically, that for cylindricity run-out then a morse taper tool should work better in the headstock because, if its been made well, then theres fewer parts to run out if that makes sense, the more variables involved, obviously its going to be much harder to keep all of them moving centrally to each other.
I use ER 20, ER 32 and ER40 collets and i would say it still relies on a good setup to perform well and isnt necessarily a magic bullet.
Michael W