I get many questions in regards to those two examples:
First when it comes to "elle est", you need to consider the fact that the last "e" in "elle" is silent and therefore doesn't clash with the "e" in "est".
As to why the "u" is allowed to remain when followed by a vowel, this is because phonetically it is not objectionable to the French ear. In street French the "u" is often dropped regardless.
In the end the clash of vowels is more a clash of vowel sounds.
This being French, you can count on many exceptions to any one rule :)
"That's French for ya!"